Contacts of the helix formed by residues 547 - 568 (chain A) in PDB entry 1P2H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLY 3.3 23.1 - - - +
173A ASN* 3.0 35.0 + - - -
236A MET* 4.2 1.5 - - - +
244A ALA* 5.0 2.9 - - - -
546A GLY* 1.4 71.1 - - - -
548A ASN* 1.3 59.5 + - - +
551A SER 3.6 6.9 + - - -
805A FAD 3.2 10.7 + - - +
806A TEO 2.6 17.8 + - - +
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Residues in contact with ASN 548 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A ASN* 2.5 35.9 + - - +
192A MET* 3.8 8.5 - - - +
196A THR* 3.0 33.1 + - - +
212A LEU* 3.8 15.5 - - - +
540A HIS* 3.7 18.4 + - + +
544A ARG* 4.2 2.5 - - + -
545A LEU* 2.9 32.9 + - - +
547A GLY* 1.3 74.8 - - - +
549A ALA* 1.3 58.5 + - - +
550A ILE 3.3 0.2 - - - -
551A SER* 3.4 2.5 + - - +
552A ASP* 2.8 27.5 + - - +
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Residues in contact with ALA 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
505A HIS* 3.6 9.0 - - + -
540A HIS* 4.2 0.9 - - - -
544A ARG* 3.5 29.3 - - - +
548A ASN* 1.3 71.0 - - - +
550A ILE* 1.3 64.5 + - - +
552A ASP* 3.2 8.3 + - - +
553A ILE* 2.9 34.4 + - + +
805A FAD 3.0 42.2 + - - +
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Residues in contact with ILE 550 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A ALA* 4.3 11.2 - - + +
168A ALA* 3.8 17.3 - - + -
171A GLY 4.1 6.7 - - - +
172A MET* 3.5 31.4 - - + +
253A VAL* 4.6 9.4 - - + -
254A GLY* 5.4 1.3 - - - -
257A VAL* 5.2 12.6 - - + -
549A ALA* 1.3 77.5 - - - +
551A SER* 1.3 64.9 + - - +
553A ILE* 3.5 24.6 + - + +
554A ILE* 3.2 28.7 + - + +
805A FAD 2.9 48.7 + - + +
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Residues in contact with SER 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A MET* 3.9 19.9 - - - +
173A ASN* 2.8 36.4 + - - -
192A MET* 3.8 7.0 - - - +
212A LEU* 3.7 14.7 + - - +
216A SER* 3.8 10.9 - - - -
219A SER* 5.6 0.2 - - - -
547A GLY 3.6 3.9 + - - -
548A ASN* 3.4 7.2 + - - -
549A ALA 3.2 0.2 - - - -
550A ILE* 1.3 81.9 - - - +
552A ASP* 1.3 61.9 + - - +
554A ILE* 3.4 1.0 + - - +
555A THR* 3.2 24.6 + - - -
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Residues in contact with ASP 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 3.5 13.3 - - + +
505A HIS* 5.7 0.3 + - - -
533A GLY* 3.6 30.8 + - - +
534A GLU* 5.1 1.0 - - - -
536A THR* 4.4 1.6 + - - -
539A VAL* 3.9 12.1 - - - +
540A HIS* 2.8 33.5 + - + +
548A ASN 2.8 18.8 + - - +
549A ALA* 3.3 7.3 - - - +
551A SER* 1.3 74.5 - - - +
553A ILE* 1.3 59.6 + - - +
554A ILE 3.1 0.7 + - - -
556A PHE* 2.8 46.9 + - - +
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Residues in contact with ILE 553 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A GLY* 3.5 25.0 - - - +
137A ALA* 3.3 30.3 - - + +
140A SER* 4.1 0.2 + - - -
165A ALA* 4.0 2.5 - - + -
257A VAL* 6.3 0.7 - - + -
533A GLY* 3.6 12.8 - - - +
534A GLU* 4.1 1.3 - - - +
549A ALA* 2.9 20.9 + - + +
550A ILE* 3.5 38.6 - - + +
552A ASP* 1.3 76.4 - - - +
554A ILE* 1.3 69.1 + - + +
557A GLY* 3.1 17.3 + - - -
805A FAD 3.3 46.4 - - - +
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Residues in contact with ILE 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 4.1 8.5 - - - +
140A SER* 3.3 19.5 - - - +
172A MET* 3.8 17.7 - - + -
219A SER* 3.7 19.7 + - - +
222A TRP* 3.9 19.7 - - + -
223A MET* 3.9 29.4 - - + -
257A VAL* 4.2 9.4 - - + -
261A LEU* 4.1 11.2 - - + -
550A ILE* 3.2 21.4 + - + +
551A SER 4.0 0.2 - - - +
552A ASP 3.2 0.4 - - - -
553A ILE* 1.3 87.5 - - + +
555A THR* 1.3 56.8 + - - +
558A ARG* 3.1 31.4 + - - +
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Residues in contact with THR 555 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.7 25.6 - - + +
212A LEU* 4.7 5.7 + - - -
215A HIS* 3.5 35.4 + - + +
216A SER* 4.4 2.6 + - - -
219A SER* 2.1 33.3 + - - +
551A SER* 3.2 15.5 + - - -
552A ASP* 4.0 1.3 - - - -
554A ILE* 1.3 76.2 - - - +
556A PHE* 1.4 66.5 - - + +
558A ARG* 4.0 3.2 - - - +
559A LEU* 3.1 26.2 + - + +
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Residues in contact with PHE 556 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208A LEU* 3.9 43.7 - - + -
211A VAL* 3.6 30.1 - - + -
212A LEU* 4.6 9.4 - - + -
512A ILE* 3.7 20.2 - - + -
513A ASP 4.8 2.9 - - - -
514A THR 4.9 1.8 - - - -
516A ALA* 4.2 0.4 - - + +
531A GLY 4.9 0.4 - - - +
532A ALA* 3.4 19.4 - - + +
533A GLY 4.3 1.1 - - - +
536A THR* 5.7 0.4 - - - +
539A VAL* 4.3 19.7 - - + -
552A ASP* 2.8 40.7 + - - +
555A THR* 1.4 77.7 - - + +
557A GLY* 1.3 56.9 + - - +
559A LEU* 3.3 20.1 - - + +
560A ALA* 2.8 35.7 + - - +
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Residues in contact with GLY 557 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137A ALA 3.5 17.5 - - - -
140A SER* 4.2 0.9 - - - -
141A ALA* 3.1 19.4 - - - +
532A ALA* 3.6 12.2 - - - +
553A ILE 3.1 19.1 + - - -
556A PHE* 1.3 75.8 - - - +
558A ARG* 1.3 64.8 + - - +
560A ALA* 3.2 0.9 + - - -
561A GLY 3.0 19.6 + - - -
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Residues in contact with ARG 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A SER* 3.8 5.9 - - - -
144A SER* 2.5 36.7 + - - -
218A ASP* 4.4 18.6 + - - +
219A SER* 5.3 6.7 + - - +
222A TRP* 3.1 67.3 - - + +
554A ILE 3.1 19.3 + - - +
555A THR* 4.0 3.6 - - - +
557A GLY* 1.3 73.6 - - - +
559A LEU* 1.3 66.5 + - + +
562A GLU* 3.4 25.0 + - + +
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Residues in contact with LEU 559 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211A VAL* 3.7 27.1 - - + -
215A HIS* 4.4 16.2 - - + -
514A THR 3.6 20.9 - - - +
515A LYS* 3.8 7.4 - - - +
516A ALA* 3.1 28.9 - - + +
555A THR 3.1 18.2 + - - +
556A PHE* 3.3 19.5 - - + +
557A GLY 3.3 0.2 - - - -
558A ARG* 1.3 81.0 - - - +
560A ALA* 1.3 63.8 + - - +
562A GLU* 3.3 9.3 + - + +
563A GLU* 2.8 35.1 + - + +
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Residues in contact with ALA 560 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310A ILE* 3.8 26.2 - - + -
515A LYS 4.5 1.8 - - - -
516A ALA* 3.7 18.2 - - + -
530A TYR* 4.0 9.9 - - + -
532A ALA* 4.2 5.8 - - + -
556A PHE 2.8 20.2 + - - +
557A GLY 3.8 3.1 - - - +
558A ARG 3.2 0.4 - - - -
559A LEU* 1.3 80.7 - - - +
561A GLY* 1.3 51.5 - - - +
563A GLU* 3.3 1.9 + - - +
564A ALA* 2.7 37.1 + - - +
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Residues in contact with GLY 561 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141A ALA 3.5 23.8 - - - -
144A SER* 3.6 4.0 - - - -
145A ALA* 3.3 15.0 - - - +
310A ILE* 3.7 11.6 - - - +
557A GLY 3.0 11.1 + - - -
558A ARG 3.5 0.2 + - - -
559A LEU 3.3 0.2 - - - -
560A ALA* 1.3 77.3 - - - +
562A GLU* 1.3 55.4 + - - +
564A ALA* 3.9 0.3 - - - +
565A ALA* 3.0 29.3 + - - +
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Residues in contact with GLU 562 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A SER* 4.1 12.6 - - - +
148A SER* 3.8 23.9 + - - +
558A ARG* 3.4 30.6 + - - +
559A LEU* 3.3 10.0 + - + +
560A ALA 3.2 0.6 - - - -
561A GLY* 1.3 73.7 - - - +
563A GLU* 1.3 74.6 + - - +
565A ALA* 4.0 0.8 - - - +
566A LYS* 3.2 31.8 + - + +
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Residues in contact with GLU 563 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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515A LYS* 2.8 65.7 + - + +
517A GLU* 5.1 1.3 - - - +
530A TYR* 3.1 20.9 + - + +
559A LEU* 2.8 25.4 + - + +
560A ALA 3.8 0.9 - - - +
562A GLU* 1.3 84.0 - - - +
564A ALA* 1.4 62.1 + - - +
566A LYS* 3.9 5.3 - - - +
567A TYR* 3.0 19.6 + - - +
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Residues in contact with ALA 564 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 4.1 8.7 - - + -
308A ALA* 3.8 13.7 - - + +
310A ILE* 3.6 20.9 - - + -
530A TYR* 3.4 28.3 - - + -
560A ALA 2.7 21.7 + - - +
561A GLY 3.9 2.5 - - - +
563A GLU* 1.4 74.5 - - - +
565A ALA* 1.3 55.5 + - - +
567A TYR* 3.4 2.6 + - - +
568A SER 3.1 28.2 + - - -
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Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A VAL* 4.4 1.1 - - - -
145A ALA* 3.9 2.9 - - + -
148A SER* 3.6 31.8 - - - +
149A GLY 5.2 2.3 - - - +
150A ALA* 3.4 32.9 - - + +
561A GLY 3.0 19.6 + - - +
562A GLU 4.2 0.7 - - - +
563A GLU 3.3 0.6 - - - -
564A ALA* 1.3 75.5 - - - +
566A LYS* 1.3 59.7 + - - +
568A SER* 3.5 14.8 + - - +
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Residues in contact with LYS 566 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 5.3 8.5 - - - +
562A GLU* 3.2 20.5 + - + +
563A GLU* 3.9 7.2 - - - +
565A ALA* 1.3 73.8 - - + +
567A TYR* 1.3 67.0 + - - +
568A SER* 3.1 5.1 + - - -
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Residues in contact with TYR 567 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A THR* 3.9 12.0 + - - +
289A VAL 5.5 0.2 + - - -
307A ASP* 3.5 21.9 + - + -
308A ALA* 4.1 9.0 - - + -
527A PRO* 3.2 24.3 - - + +
528A GLY* 3.1 40.3 + - - -
530A TYR* 3.2 25.6 - - - +
563A GLU 3.0 9.8 + - - +
564A ALA 3.5 3.1 - - - +
566A LYS* 1.3 76.0 - - - +
568A SER* 1.3 63.7 + - - +
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Residues in contact with SER 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A ASP* 3.1 37.2 + - - +
129A VAL* 4.7 0.3 - - - +
150A ALA* 5.0 0.3 - - - +
307A ASP* 3.4 39.0 + - - +
308A ALA* 5.2 0.7 - - - -
564A ALA 3.1 15.6 + - - -
565A ALA* 3.5 17.3 + - - +
566A LYS 4.2 3.1 - - - -
567A TYR* 1.3 82.2 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il