Contacts of the helix formed by residues 636 - 646 (chain B) in PDB entry 1PG3
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 636 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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634B ASP* 2.8 16.8 + - - -
635B PRO* 1.3 74.6 - - - +
637B VAL* 1.3 64.0 + - - +
638B VAL 3.2 2.5 + - - -
639B GLU* 3.6 8.4 + - - +
640B LYS* 3.5 17.7 + - - +
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Residues in contact with VAL 637 (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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601B SER* 3.1 47.1 - - - +
602B LEU 4.4 6.1 - - - +
603B PRO* 3.8 29.2 - - + -
632B LEU* 4.4 2.0 - - + -
634B ASP* 3.3 33.0 + - + +
636B GLY* 1.3 75.1 - - - +
638B VAL* 1.3 65.3 + - + +
640B LYS* 3.3 1.9 + - - +
641B LEU* 2.7 41.4 + - + +
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Residues in contact with VAL 638 (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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614B ILE* 4.9 11.9 - - + -
618B ILE* 4.2 16.6 - - + +
629B THR* 3.5 29.6 - - + +
632B LEU* 3.9 19.5 - - + -
635B PRO 3.3 17.5 - - - +
636B GLY 3.2 0.2 - - - -
637B VAL* 1.3 79.1 - - + +
639B GLU* 1.3 62.4 + - - +
641B LEU* 3.7 7.0 - - - +
642B LEU* 3.1 37.3 + - + +
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Residues in contact with GLU 639 (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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635B PRO 4.5 0.6 + - - +
636B GLY* 3.6 9.6 + - - +
637B VAL 3.4 0.4 - - - -
638B VAL* 1.3 79.2 - - - +
640B LYS* 1.3 62.2 + - - +
642B LEU* 3.3 15.0 + - + +
643B GLU* 3.2 21.7 + - - +
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Residues in contact with LYS 640 (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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601B SER* 3.9 19.1 - - - +
636B GLY 3.5 10.5 + - - +
637B VAL* 3.3 7.5 + - - +
639B GLU* 1.3 75.8 - - - +
641B LEU* 1.3 64.2 + - - +
642B LEU 3.3 0.2 + - - -
643B GLU* 3.3 7.1 + - - +
644B GLU* 3.1 33.2 + - + +
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Residues in contact with LEU 641 (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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562B TYR* 4.5 4.3 - - + -
597B HIS* 3.8 14.3 - - + -
599B THR* 3.3 23.6 - - + +
601B SER* 3.3 24.7 - - - +
602B LEU* 5.3 0.2 - - - -
603B PRO* 3.6 21.3 - - + -
614B ILE* 6.0 0.9 - - + -
615B LEU* 3.6 16.8 - - + -
618B ILE* 4.0 20.8 - - + +
637B VAL* 2.7 30.4 + - + +
638B VAL* 3.7 4.9 - - - +
640B LYS* 1.3 73.9 - - - +
642B LEU* 1.3 57.0 + - - +
644B GLU* 3.3 19.7 - - - +
645B LYS* 3.0 29.3 + - - +
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Residues in contact with LEU 642 (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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618B ILE* 3.8 32.1 - - + +
638B VAL* 3.1 32.8 + - + +
639B GLU* 3.3 16.4 - - - +
641B LEU* 1.3 73.6 - - - +
643B GLU* 1.3 54.3 + - - +
645B LYS* 2.9 10.0 + - + +
646B GLN* 2.8 34.5 + - - +
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Residues in contact with GLU 643 (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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639B GLU 3.2 9.1 + - - +
640B LYS* 3.7 9.4 - - - +
642B LEU* 1.3 77.8 - - - +
644B GLU* 1.3 64.5 + - + +
646B GLN* 3.0 25.7 + - - +
647B ALA* 3.4 8.3 + - - +
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Residues in contact with GLU 644 (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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597B HIS* 3.0 31.4 + - + +
598B TRP 3.8 8.2 - - - +
599B THR* 2.8 32.5 + - - -
600B ASP 4.7 1.4 + - - -
601B SER* 4.9 4.2 + - - -
640B LYS* 3.1 19.1 + - + +
641B LEU* 3.3 14.5 - - - +
643B GLU* 1.3 76.5 - - + +
645B LYS* 1.3 60.8 + - - +
647B ALA* 3.1 24.5 + - - +
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Residues in contact with LYS 645 (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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560B TYR* 3.6 25.1 - - + +
597B HIS* 4.1 9.8 - - + -
618B ILE* 3.7 28.6 + - + +
619B ALA* 3.3 29.1 + - - +
621B GLY* 4.6 9.7 - - - -
641B LEU 3.0 15.1 + - - +
642B LEU* 2.9 12.0 + - + +
644B GLU* 1.3 70.9 - - - +
646B GLN* 1.3 59.1 + - - +
647B ALA 3.0 17.0 + - - +
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Residues in contact with GLN 646 (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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642B LEU 2.8 11.5 + - - +
643B GLU* 3.0 17.2 + - - +
645B LYS* 1.3 76.6 - - - +
647B ALA* 1.3 58.0 + - - +
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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
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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