Contacts of the helix formed by residues 544 - 558 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B LEU* 3.4 10.2 - - - +
522B MET* 5.8 0.2 - - - -
542B VAL* 4.4 0.3 - - - +
543B PRO* 1.3 84.4 - - - +
545B PRO* 1.4 71.9 - - - +
546B THR* 3.7 12.0 + - - -
547B ALA* 3.1 18.7 + - - +
548B ALA* 2.9 29.5 + - - +
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Residues in contact with PRO 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.8 9.1 - - + -
126B PHE 5.8 0.2 - - - +
129B ASN* 3.9 41.3 - - + +
130B ALA* 4.6 0.7 - - + -
133B ALA* 3.6 26.1 - - + +
264B SER* 4.9 0.3 - - - -
544B SER* 1.4 88.9 - - - +
546B THR* 1.3 65.0 + - - +
548B ALA* 3.3 6.2 + - + +
549B THR* 3.0 27.4 + - - -
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Residues in contact with THR 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B ASP 5.0 1.6 - - - +
141B ALA* 3.5 38.4 - - + +
144B GLY* 6.1 2.5 - - - -
145B THR* 4.9 7.2 - - - +
522B MET* 6.0 2.0 - - - -
544B SER* 3.8 12.0 + - - -
545B PRO* 1.3 75.8 - - - +
547B ALA* 1.3 66.6 + - - +
549B THR* 2.9 14.8 + - - -
550B LEU* 3.2 19.8 + - + +
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Residues in contact with ALA 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
522B MET* 3.9 16.4 - - + -
525B MET* 3.4 25.3 - - + +
542B VAL* 3.9 3.8 - - + -
543B PRO* 3.5 32.5 - - + -
544B SER* 3.1 13.3 + - - +
546B THR* 1.3 78.1 - - - +
548B ALA* 1.3 52.7 + - - +
550B LEU 3.2 0.2 + - - -
551B HIS* 2.7 37.9 + - - +
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Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 3.5 9.2 - - + +
117B LEU* 5.0 0.9 - - + -
264B SER* 3.8 5.2 - - - -
265B ALA* 4.0 28.9 - - + +
542B VAL* 3.6 23.5 - - + +
544B SER 2.9 13.4 + - - +
545B PRO* 3.4 12.6 - - + +
546B THR 3.1 0.2 - - - -
547B ALA* 1.3 76.6 - - - +
549B THR* 1.3 62.7 + - - +
552B ALA* 3.0 23.6 + - - +
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Residues in contact with THR 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B GLY* 3.5 20.7 - - - +
137B SER 3.6 29.6 + - - +
138B LEU* 3.9 14.9 - - + +
141B ALA* 4.0 11.2 - - + -
262B LEU* 3.4 23.9 - - + +
264B SER* 2.9 21.7 + - - +
545B PRO 3.0 12.3 + - - -
546B THR* 2.9 11.1 + - - -
548B ALA* 1.3 77.4 - - - +
550B LEU* 1.3 60.9 + - - +
552B ALA* 3.6 4.9 - - - +
553B LEU* 4.0 3.3 + - - +
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Residues in contact with LEU 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.4 4.5 - - + -
141B ALA* 3.8 18.2 - - + +
142B LEU* 3.7 29.4 - - + -
145B THR* 4.0 15.3 - - + +
147B VAL* 4.1 6.3 - - + -
522B MET* 3.7 37.5 - - + -
525B MET* 3.6 15.0 - - + -
526B VAL* 4.0 12.9 - - + +
546B THR* 3.2 16.2 + - + +
547B ALA 3.7 0.4 - - - +
549B THR* 1.3 78.5 - - - +
551B HIS* 1.3 60.3 + - - +
553B LEU* 2.9 40.6 - - + +
554B HIS* 4.2 2.8 + - - -
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Residues in contact with HIS 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 3.9 13.5 - - + -
525B MET* 3.9 6.6 - - + +
529B LYS* 3.6 32.0 - - + -
532B GLN* 4.5 0.2 - - - -
533B PRO* 3.7 20.0 - - + -
540B ALA* 3.8 10.7 - - - +
542B VAL* 3.5 17.9 - - + -
547B ALA 2.7 21.4 + - - +
550B LEU* 1.3 67.8 - - - +
552B ALA* 1.3 52.4 + - - +
553B LEU 2.8 4.0 - - - -
554B HIS* 2.6 72.5 + - - +
555B TYR* 2.7 44.0 + + - -
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Residues in contact with ALA 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B PRO* 3.6 12.0 - - + +
237B LEU* 4.5 2.9 - - + +
262B LEU* 4.2 9.2 - - + -
263B GLU 3.6 23.6 - - - +
264B SER* 4.1 5.8 - - - -
548B ALA 3.0 20.1 + - - +
549B THR 3.6 9.9 - - - +
551B HIS* 1.3 75.3 - - - +
553B LEU* 1.3 62.4 + - - +
554B HIS 3.1 0.9 + - - -
555B TYR* 3.1 17.4 + - - +
556B HIS* 3.2 20.7 + - + -
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Residues in contact with LEU 553 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B LEU* 3.8 25.6 - - + -
142B LEU* 5.5 0.2 - - + -
147B VAL* 5.8 0.2 - - + -
171B TYR* 4.3 25.1 - - + +
175B PHE* 4.3 23.6 - - + -
262B LEU* 3.9 13.5 - - + -
526B VAL* 4.1 19.1 - - + -
550B LEU* 2.9 41.8 + - + +
551B HIS 2.7 0.6 + - - -
552B ALA* 1.3 78.2 - - - +
554B HIS* 1.3 65.9 + - + +
556B HIS* 3.5 11.6 - - - +
557B GLN* 3.4 28.9 + - - +
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Residues in contact with HIS 554 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B MET* 3.4 21.8 - - + -
526B VAL* 2.8 36.5 + - + +
529B LYS* 3.7 4.7 - - + -
530B ILE* 3.4 35.2 + - + -
533B PRO* 3.7 20.2 - - + -
550B LEU 4.5 3.6 + - - -
551B HIS* 2.6 51.2 + - + +
553B LEU* 1.3 74.9 - - + +
555B TYR* 1.3 56.2 + - - +
557B GLN* 3.0 11.9 + - - -
558B VAL* 2.9 34.6 + - - +
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Residues in contact with TYR 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B ALA* 3.7 16.8 - - + +
114B GLY* 3.7 18.1 + - - -
115B PRO* 3.6 19.3 - - + -
235B HIS* 2.8 22.7 + - + +
237B LEU* 3.5 22.2 - - + -
533B PRO* 4.1 16.9 - - + +
537B ALA 4.3 3.7 + - - -
538B SER 3.9 13.7 - - - -
539B THR* 3.5 2.4 - - - -
540B ALA* 3.1 23.0 + - - +
551B HIS* 2.7 56.7 + + - -
552B ALA* 3.1 3.8 + - - +
554B HIS* 1.3 76.0 - - + +
556B HIS* 1.3 51.2 + - - +
558B VAL* 2.6 24.4 - - - +
560B VAL* 4.0 14.5 - - + +
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Residues in contact with HIS 556 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PHE* 3.7 30.0 - + + -
179B SER* 3.8 8.1 + - - +
234B ASN* 3.1 46.4 + - - +
235B HIS* 3.3 11.8 - - - -
237B LEU* 3.6 40.0 - - + +
238B HIS 4.7 2.0 + - - -
239B ILE* 3.7 26.4 - - + +
262B LEU* 4.7 10.0 - - + +
263B GLU 5.1 3.2 + - - -
552B ALA* 3.2 24.6 + - + -
553B LEU* 3.5 9.4 - - - +
555B TYR* 1.3 79.4 - - - +
557B GLN* 1.4 57.1 + - + +
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Residues in contact with GLN 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175B PHE* 6.6 0.2 - - + -
178B ASP* 6.6 0.4 - - + -
179B SER* 6.1 0.4 - - - +
235B HIS* 4.2 3.2 - - - -
526B VAL* 5.4 6.5 + - - +
530B ILE* 3.2 26.7 - - - +
534B ARG* 4.7 4.0 + - - -
553B LEU* 3.4 21.5 + - - +
554B HIS* 3.0 16.2 + - - +
556B HIS* 1.4 76.7 - - + +
558B VAL* 1.3 67.5 + - + +
559B ASP 4.0 1.0 + - - -
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Residues in contact with VAL 558 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B HIS* 3.1 3.5 + - - +
530B ILE* 3.8 28.0 - - + -
533B PRO* 3.6 38.8 - - + +
534B ARG* 3.9 23.3 - - + +
554B HIS 2.9 15.8 + - - +
555B TYR* 2.6 27.0 - - - +
557B GLN* 1.3 80.8 - - - +
559B ASP* 1.3 63.1 + - - +
560B VAL* 3.4 7.8 + - + +
563B VAL* 4.0 15.0 - - + -
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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
------------------------------------------------------------
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