Contacts of the helix formed by residues 643 - 658 (chain B) in PDB entry 4G3D
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 643 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575B ALA* 6.4 2.5 - - - -
576B LYS* 3.8 14.9 - - - +
579B VAL* 4.0 4.7 - - - -
642B VAL* 1.3 76.6 - - - +
644B ALA* 1.3 65.0 + - - +
645B ALA* 3.9 7.5 + - - +
646B GLU* 3.4 23.9 + - - +
647B LEU* 3.0 22.2 + - - +
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Residues in contact with ALA 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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500B LEU* 3.7 46.1 - - + +
503B LEU* 4.2 5.4 - - + -
504B GLU* 3.8 15.9 - - - +
507B HIS* 4.1 18.1 + - + +
575B ALA* 6.3 0.2 - - - +
579B VAL* 3.8 9.8 - - + +
643B SER* 1.3 73.1 - - - +
645B ALA* 1.3 53.4 + - - +
647B LEU* 3.3 1.8 + - - +
648B GLY* 2.8 33.4 + - - -
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Residues in contact with ALA 645 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B GLU* 3.3 40.1 - - + +
643B SER* 3.3 7.9 + - - +
644B ALA* 1.3 78.3 - - - +
646B GLU* 1.3 62.8 + - - +
648B GLY* 3.2 2.9 + - - -
649B GLY* 3.2 17.5 + - - -
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Residues in contact with GLU 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 VAL* 3.4 28.5 - - + +
643B SER* 3.3 19.5 + - - +
644B ALA 3.3 0.4 - - - -
645B ALA* 1.3 78.0 - - - +
647B LEU* 1.3 61.8 + - - +
649B GLY* 3.4 3.6 + - - -
650B LYS* 3.2 46.8 + - - +
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Residues in contact with LEU 647 (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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496B LEU* 5.1 2.2 - - + -
500B LEU* 3.9 30.5 - - + -
579B VAL* 4.1 14.6 - - + -
582B SER* 4.3 1.3 - - - +
583B CYS* 3.7 25.8 - - - -
629B ALA* 3.3 42.8 - - + +
632B GLU* 5.2 0.2 - - + -
633B GLY* 4.6 0.2 - - - -
642B VAL* 4.0 17.2 - - + +
643B SER 3.0 16.2 + - - +
644B ALA* 3.7 4.7 - - - +
646B GLU* 1.3 73.6 - - - +
648B GLY* 1.3 55.4 + - - +
650B LYS* 3.2 8.7 + - + +
651B VAL* 2.8 41.6 + - + +
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Residues in contact with GLY 648 (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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497B GLY* 5.4 6.1 - - - -
500B LEU* 4.0 17.9 - - - +
501B GLU* 6.4 1.6 - - - -
504B GLU* 6.1 0.4 - - - -
644B ALA 2.8 16.8 + - - -
645B ALA* 3.2 3.5 + - - -
647B LEU* 1.3 73.4 - - - +
649B GLY* 1.3 63.0 + - - +
651B VAL* 3.9 2.5 - - - +
652B ASN* 3.0 26.9 + - - +
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Residues in contact with GLY 649 (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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645B ALA 3.2 11.7 + - - -
646B GLU 3.4 4.5 + - - -
647B LEU 3.2 0.2 - - - -
648B GLY* 1.3 76.4 - - - +
650B LYS* 1.3 62.2 + - - +
652B ASN* 3.7 4.5 - - - +
653B ARG* 2.9 28.8 + - - +
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Residues in contact with LYS 650 (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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625B LEU* 3.7 19.3 - - + +
628B GLN* 4.9 7.4 - - - +
629B ALA* 4.0 20.2 - - + +
632B GLU* 2.9 35.1 + - - +
642B VAL* 5.2 0.7 - - + -
646B GLU* 3.2 49.5 + - + +
647B LEU* 3.2 15.3 + - + +
649B GLY* 1.3 73.6 - - - +
651B VAL* 1.3 55.9 + - - +
653B ARG* 3.4 21.7 + - - +
654B ALA* 2.9 28.9 + - - +
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Residues in contact with VAL 651 (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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493B LEU* 3.4 41.2 - - + +
496B LEU* 3.6 26.5 - - + -
497B GLY* 3.8 17.0 - - - +
500B LEU* 4.0 8.1 - - + -
629B ALA* 4.5 10.8 - - + -
647B LEU* 2.8 29.8 + - + +
648B GLY* 3.9 5.8 - - - +
650B LYS* 1.3 69.8 - - - +
652B ASN* 1.3 63.0 + - - +
654B ALA* 3.1 8.5 + - - +
655B LEU* 2.9 27.9 + - + +
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Residues in contact with ASN 652 (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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497B GLY* 6.5 0.4 - - - -
648B GLY 3.0 18.3 + - - +
649B GLY* 3.7 4.0 - - - +
651B VAL* 1.3 78.6 - - - +
653B ARG* 1.3 62.1 + - - +
655B LEU* 3.4 16.9 + - - +
656B GLN* 3.3 21.4 + - - +
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Residues in contact with ARG 653 (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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625B LEU* 4.0 36.6 - - + +
628B GLN* 5.5 3.4 + - - -
649B GLY 2.9 18.5 + - - +
650B LYS* 3.4 23.6 - - - +
652B ASN* 1.3 78.2 + - - +
654B ALA* 1.3 61.0 + - - +
656B GLN* 3.5 7.9 + - + +
657B GLN* 3.2 19.6 + - - +
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Residues in contact with ALA 654 (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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493B LEU* 3.9 11.7 - - + -
623B ALA* 5.3 0.2 - - - +
625B LEU* 4.1 7.6 - - + +
626B THR* 3.7 34.3 - - - +
629B ALA* 5.7 0.4 - - + -
650B LYS 2.9 14.5 + - - +
651B VAL* 3.1 8.9 + - - +
653B ARG* 1.3 75.9 - - - +
655B LEU* 1.3 63.8 + - - +
657B GLN* 3.1 12.7 + - - +
658B VAL* 3.0 26.0 + - - +
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Residues in contact with LEU 655 (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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490B ASP* 3.9 11.9 - - - +
493B LEU* 3.8 14.5 - - + +
494B TYR* 3.7 47.8 - - + +
651B VAL* 2.9 12.9 + - + +
652B ASN* 3.6 21.8 - - - +
653B ARG 3.3 0.2 - - - -
654B ALA* 1.3 76.6 - - - +
656B GLN* 1.3 62.9 + - - +
658B VAL* 3.3 10.8 - - - +
660B GLY* 2.8 51.5 + - - -
661B LEU* 3.9 7.2 - - + +
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Residues in contact with GLN 656 (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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652B ASN* 3.3 10.6 + - - +
653B ARG* 3.8 10.5 - - + +
654B ALA 3.2 0.2 - - - -
655B LEU* 1.3 88.8 - - - +
657B GLN* 1.3 63.0 + - - +
659B GLY* 3.2 14.7 + - - -
660B GLY* 4.2 7.3 - - - +
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Residues in contact with GLN 657 (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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623B ALA* 3.9 10.8 - - + +
624B PRO* 3.4 31.5 - - - +
625B LEU* 2.8 40.7 - - + +
653B ARG 3.2 10.0 + - - +
654B ALA* 3.1 9.6 + - - +
656B GLN* 1.3 80.3 - - - +
658B VAL* 1.3 58.5 + - + +
659B GLY* 3.1 5.0 + - - -
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Residues in contact with VAL 658 (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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489B GLU* 3.8 24.2 - - + +
490B ASP* 3.9 31.0 - - + +
493B LEU* 4.0 3.6 - - + -
623B ALA* 3.7 29.2 - - + -
626B THR* 4.5 1.6 - - - +
654B ALA 3.0 15.2 + - - +
655B LEU* 3.3 20.0 - - - +
657B GLN* 1.3 72.7 - - - +
659B GLY* 1.3 55.3 + - - +
660B GLY 4.5 2.0 - - - +
662B LYS* 5.6 2.4 - - - +
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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