Contacts of the helix formed by residues 544 - 558 (chain A) in PDB entry 2GQ3
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 SER 544 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.3 15.4 - - - +
519A THR* 5.5 3.4 + - - -
522A MET* 5.5 1.4 - - - +
542A VAL* 3.9 0.5 - - - +
543A PRO* 1.4 81.5 - - - +
545A PRO* 1.4 70.6 - - - +
546A THR* 3.7 8.8 + - - +
547A ALA* 3.2 23.2 + - - +
548A ALA* 2.9 23.9 + - - +
800A COA 3.9 16.8 - - - -
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Residues in contact with PRO 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LEU* 4.0 2.2 - - + -
129A ASN* 4.0 19.1 - - - +
133A ALA* 3.9 24.5 - - + +
544A SER* 1.4 84.5 - - - +
546A THR* 1.3 65.9 + - - +
548A ALA* 3.0 16.0 + - + +
549A THR* 3.0 17.9 + - - -
800A COA 3.4 44.9 - - + +
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Residues in contact with THR 546 (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 ASP 5.9 0.5 - - - -
141A ALA* 4.2 18.0 - - + +
145A THR* 3.4 33.0 - - + -
522A MET* 4.8 3.8 - - + -
544A SER* 3.3 8.9 + - - +
545A PRO* 1.3 77.8 - - - +
547A ALA* 1.3 62.2 + - - +
549A THR* 3.3 6.9 + - - -
550A LEU* 3.1 27.6 + - + +
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Residues in contact with ALA 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522A MET* 3.9 18.1 - - + -
525A MET* 3.4 18.4 - - - +
542A VAL* 3.7 4.1 - - + +
543A PRO* 3.7 26.9 - - + -
544A SER* 3.2 21.8 + - - +
546A THR* 1.3 81.1 - - - +
548A ALA* 1.3 54.8 + - - +
551A HIS* 2.9 32.1 + - - +
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Residues in contact with ALA 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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115A PRO* 3.4 14.5 - - + +
117A LEU* 5.2 1.3 - - + -
133A ALA 4.9 0.7 - - - +
264A SER* 3.7 17.1 - - - -
265A ALA* 4.2 17.5 - - + +
542A VAL* 3.8 19.7 - - + +
544A SER 2.9 13.0 + - - +
545A PRO* 3.0 13.2 + - + +
547A ALA* 1.3 71.7 - - - +
549A THR* 1.3 62.8 + - - +
551A HIS 3.5 0.2 + - - -
552A ALA* 2.9 27.0 + - - +
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Residues in contact with THR 549 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A GLY* 3.8 23.1 - - - +
137A SER 4.0 6.6 + - - +
138A LEU* 3.9 30.7 - - + -
141A ALA* 4.0 9.6 - - + -
262A LEU* 3.3 28.1 - - + +
264A SER* 3.2 20.4 + - - +
545A PRO 3.0 12.5 + - - -
546A THR* 3.6 9.2 - - - -
548A ALA* 1.3 76.1 - - - +
550A LEU* 1.3 63.7 + - - +
552A ALA* 3.4 7.3 + - - +
553A LEU* 3.8 1.0 + - - +
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Residues in contact with LEU 550 (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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138A LEU* 4.4 3.4 - - + -
141A ALA* 3.8 22.2 - - + +
142A LEU* 3.7 30.7 - - + -
145A THR* 4.2 5.4 - - - +
147A VAL* 3.7 25.6 - - + -
522A MET* 3.7 28.9 - - + -
525A MET* 3.6 14.4 - - + -
526A VAL* 3.9 9.6 - - + +
546A THR* 3.1 17.6 + - + +
548A ALA 3.2 0.2 - - - -
549A THR* 1.3 76.6 - - - +
551A HIS* 1.3 65.0 + - - +
552A ALA 3.1 0.9 - - - -
553A LEU* 2.9 37.9 + - + +
554A HIS* 4.2 2.6 + - - -
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Residues in contact with HIS 551 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO* 3.9 12.1 - - + -
525A MET* 3.6 8.6 - - + +
529A LYS* 3.6 44.7 - - + +
532A GLN* 4.5 0.7 - - - -
533A PRO* 4.0 7.6 - - + -
540A ALA* 3.6 9.1 - - - +
542A VAL* 3.6 17.7 - - + -
547A ALA 2.9 22.1 + - - +
548A ALA 4.0 3.1 - - - +
550A LEU* 1.3 74.1 - - - +
552A ALA* 1.3 63.1 + - - +
553A LEU 2.9 1.6 + - - -
554A HIS* 2.9 47.1 + - + +
555A TYR* 2.9 45.6 + + - -
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Residues in contact with ALA 552 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A PRO* 3.6 11.4 - - + +
237A LEU* 5.0 2.2 - - + -
262A LEU* 4.2 11.2 - - + -
263A GLU 3.9 20.9 - - - +
264A SER* 4.2 6.7 - - - -
548A ALA 2.9 14.8 + - - +
549A THR* 3.4 13.7 - - - +
550A LEU 3.1 0.6 - - - -
551A HIS* 1.3 75.8 - - - +
553A LEU* 1.3 63.2 + - - +
555A TYR* 3.0 18.6 + - - +
556A HIS* 3.0 21.7 + - + +
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Residues in contact with LEU 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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138A LEU* 4.1 12.6 - - + -
171A TYR* 4.0 29.8 - - + +
175A PHE* 3.5 37.1 - - + -
262A LEU* 3.9 14.4 - - + -
526A VAL* 4.4 11.4 - - + -
549A THR 4.2 5.8 - - - +
550A LEU* 2.9 36.8 + - + +
551A HIS 2.9 0.8 - - - -
552A ALA* 1.3 78.0 - - - +
554A HIS* 1.3 62.2 + - + +
556A HIS* 3.0 24.1 + - - +
557A GLN* 3.2 20.3 + - - +
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Residues in contact with HIS 554 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525A MET* 3.4 23.6 - - + -
526A VAL* 2.7 35.4 + - + +
529A LYS* 3.9 3.4 - - + -
530A ILE* 3.5 36.4 + - + -
533A PRO* 4.1 15.4 - - + +
550A LEU 4.7 1.3 - - - -
551A HIS* 2.9 46.2 + - + +
553A LEU* 1.3 83.1 - - + +
555A TYR* 1.3 56.3 + - + +
557A GLN* 3.8 13.2 - - - +
558A VAL* 2.9 35.2 + - - +
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Residues in contact with TYR 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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113A ALA* 3.7 12.3 - - + +
114A GLY* 3.6 27.0 + - - -
115A PRO* 3.8 17.7 - - + -
235A HIS* 2.9 27.8 + - + +
237A LEU* 3.6 18.6 - - + -
533A PRO* 4.0 20.0 - - + +
537A ALA* 4.1 2.0 + - - +
538A SER 3.6 14.4 - - - -
539A THR 3.5 2.4 - - - -
540A ALA* 3.2 22.2 + - - +
551A HIS* 2.9 57.5 + + - -
552A ALA* 3.0 7.9 + - - +
554A HIS* 1.3 76.0 - - + +
556A HIS* 1.3 59.8 + - - +
558A VAL* 3.0 11.2 - - - +
560A VAL* 4.1 9.0 - - + -
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Residues in contact with HIS 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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175A PHE* 3.8 22.5 - + + -
178A ASP 5.4 1.7 - - - +
179A SER* 3.6 20.9 + - - +
234A ASN* 3.1 35.5 + - - +
235A HIS* 3.3 16.0 - - - -
237A LEU* 3.7 35.4 - - + +
238A HIS 4.8 1.6 + - - -
239A ILE* 3.5 28.9 - - + +
262A LEU* 4.6 6.3 - - + +
263A GLU 5.0 2.0 + - - -
552A ALA* 3.0 31.4 + - + +
553A LEU* 3.0 8.4 + - - +
555A TYR* 1.3 76.8 - - - +
557A GLN* 1.3 63.3 + - + +
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Residues in contact with GLN 557 (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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175A PHE* 6.5 1.1 - - + -
178A ASP* 6.0 6.3 - - + +
235A HIS* 4.5 2.6 - - - -
526A VAL* 5.7 2.6 + - - +
530A ILE* 3.6 29.2 - - + +
534A ARG* 4.8 5.7 + - - +
553A LEU* 3.2 16.9 + - - +
554A HIS* 3.3 18.1 + - - +
556A HIS* 1.3 78.7 - - + +
558A VAL* 1.3 62.7 + - + +
559A ASP 3.9 1.4 + - - -
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Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235A HIS* 3.5 3.2 + - - +
530A ILE* 3.8 19.3 - - + -
533A PRO* 3.8 26.2 - - + +
534A ARG* 3.7 30.7 - - + +
554A HIS 2.9 17.0 + - - +
555A TYR* 3.0 21.7 - - - +
557A GLN* 1.3 80.2 - - + +
559A ASP* 1.3 62.5 + - - +
560A VAL* 3.2 9.7 + - + +
563A VAL* 3.7 26.9 - - + -
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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
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Atomic class I II III IV V VI VII VIII
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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