Contacts of the helix formed by residues 640 - 660 (chain A) in PDB entry 6AGF
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 GLN 640 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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632A MET* 4.6 20.7 - - - +
636A GLU* 4.1 6.4 + - - +
637A TYR* 4.0 11.0 + - - +
639A GLN* 1.3 80.7 - - - +
641A GLY* 1.3 66.2 + - - +
642A TRP* 3.5 1.9 + - - +
643A ASN* 2.4 35.5 + - - +
644A ILE* 3.8 12.1 - - - +
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Residues in contact with GLY 641 (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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639A GLN 4.0 0.9 + - - -
640A GLN* 1.3 75.7 - - - +
642A TRP* 1.3 66.6 + - - +
643A ASN 3.3 0.5 + - - -
644A ILE* 3.4 20.4 + - - +
645A PHE* 3.6 9.2 + - - +
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Residues in contact with TRP 642 (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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640A GLN* 3.5 2.2 - - - +
641A GLY* 1.3 80.0 - - - +
643A ASN* 1.3 60.7 + - - +
645A PHE* 3.1 30.7 + + + +
646A ASP* 3.0 37.1 + - - +
677A PHE* 3.4 32.1 - - + -
678A LYS* 4.5 5.6 - - + -
680A ALA* 3.6 20.6 - - + -
681A LYS* 4.0 39.4 - - + +
687A ASN* 5.6 5.4 - - - -
690A ILE* 4.2 15.5 - - + -
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Residues in contact with ASN 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A LYS* 5.3 7.1 - - - +
637A TYR* 3.3 56.5 + - + +
638A PHE* 5.1 0.7 - - - -
640A GLN* 2.4 42.0 + - - +
641A GLY 3.3 1.0 - - - -
642A TRP* 1.3 77.8 - - - +
644A ILE* 1.3 56.9 + - - +
646A ASP* 3.6 15.9 + - - +
647A SER* 2.6 33.3 + - - -
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Residues in contact with ILE 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A PHE* 3.5 40.2 - - + +
639A GLN 4.8 2.9 - - - +
640A GLN 3.8 14.6 - - - +
641A GLY* 3.7 12.8 - - - +
643A ASN* 1.3 77.5 - - - +
645A PHE* 1.3 61.3 + - - +
647A SER* 3.3 15.3 + - - -
648A ILE* 3.4 25.3 + - + +
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Residues in contact with PHE 645 (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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641A GLY 3.6 5.0 + - - +
642A TRP* 3.1 35.4 + + + +
644A ILE* 1.3 81.5 - - - +
646A ASP* 1.3 72.2 + - - +
647A SER 3.4 0.3 + - - -
648A ILE* 3.6 16.0 + - + +
649A ILE* 3.6 38.2 - - + +
674A LEU* 3.3 40.8 - - + -
677A PHE* 4.5 10.8 - + + -
678A LYS* 4.1 16.8 - - + -
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Residues in contact with ASP 646 (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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624A GLU* 6.2 0.4 - - - +
625A MET* 5.3 5.8 - - + -
637A TYR* 4.8 5.3 + - - +
642A TRP* 3.0 21.4 + - - +
643A ASN* 3.6 23.8 + - - +
644A ILE 3.3 0.2 - - - -
645A PHE* 1.3 82.5 - - - +
647A SER* 1.3 63.9 + - - +
649A ILE* 3.5 3.9 + - - +
650A VAL* 3.2 30.1 + - + +
678A LYS* 3.3 41.4 + - - +
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Residues in contact with SER 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
625A MET* 3.3 30.4 - - - +
637A TYR* 3.8 1.6 + - - -
638A PHE* 3.8 17.6 - - - -
643A ASN 2.6 22.3 + - - -
644A ILE* 3.3 8.0 + - - -
645A PHE 3.2 0.8 - - - -
646A ASP* 1.3 76.1 - - - +
648A ILE* 1.3 58.6 + - - +
650A VAL* 4.1 4.0 - - - +
651A THR* 2.6 35.1 + - - -
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Residues in contact with ILE 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A ILE* 3.4 26.2 + - + +
645A PHE* 3.6 12.1 + - + +
646A ASP 3.3 0.4 - - - -
647A SER* 1.3 78.0 - - - +
649A ILE* 1.3 55.5 + - + +
651A THR* 3.2 6.2 + - - -
652A LEU* 2.7 55.5 + - + +
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Residues in contact with ILE 649 (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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645A PHE* 3.6 51.1 + - + +
646A ASP 3.5 6.8 + - - +
647A SER 3.3 0.2 - - - -
648A ILE* 1.3 78.3 - - + +
650A VAL* 1.3 60.4 + - + +
652A LEU* 4.0 7.7 - - + +
653A SER* 2.8 33.9 + - - -
671A PHE* 4.2 18.4 - - - +
672A ARG* 4.3 4.5 - - - -
674A LEU* 4.3 15.5 - - + -
675A ARG* 3.4 46.7 - - + +
678A LYS* 4.6 4.3 - - - +
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Residues in contact with VAL 650 (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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621A PHE* 3.5 31.0 - - + +
622A THR* 3.7 27.1 - - + +
625A MET* 4.4 20.9 - - + -
626A VAL* 6.4 0.7 - - + -
646A ASP* 3.2 18.9 + - + +
647A SER* 4.1 5.8 - - - +
649A ILE* 1.3 77.3 - - + +
651A THR* 1.3 62.2 + - - +
653A SER* 3.1 16.7 + - - -
654A LEU* 3.2 17.0 + - + +
675A ARG* 4.9 4.9 - - - +
678A LYS* 6.1 2.5 - - - +
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Residues in contact with THR 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A SER 2.6 24.4 + - - -
648A ILE* 3.4 6.9 - - - -
650A VAL* 1.3 78.9 - - - +
652A LEU* 1.3 61.2 + - + +
654A LEU* 3.0 6.1 + - - +
655A VAL* 2.8 43.3 + - + +
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Residues in contact with LEU 652 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648A ILE* 2.7 41.9 + - + +
649A ILE* 4.0 7.2 - - + +
651A THR* 1.3 75.1 - - + +
653A SER* 1.3 58.1 + - - +
655A VAL* 3.8 12.9 - - + +
656A GLU* 3.1 28.4 + - - +
668A LEU* 3.8 29.3 - - + +
671A PHE* 3.9 32.5 - - + -
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Residues in contact with SER 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618A THR* 4.0 14.2 + - - +
622A THR* 5.2 0.2 - - - +
649A ILE 2.8 20.2 + - - -
650A VAL* 3.1 14.4 + - - -
652A LEU* 1.3 77.5 - - - +
654A LEU* 1.3 66.8 + - - +
656A GLU* 4.0 8.6 - - - +
657A LEU* 3.3 25.5 + - - +
668A LEU 5.4 2.9 - - - -
672A ARG* 5.0 15.9 - - - -
675A ARG* 3.9 16.6 + - - -
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Residues in contact with LEU 654 (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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618A THR* 3.8 10.8 - - + -
622A THR* 3.7 27.4 - - + -
650A VAL* 3.2 23.5 + - + +
651A THR* 3.0 5.9 + - - +
653A SER* 1.3 89.1 + - - +
655A VAL* 1.3 56.2 + - - +
656A GLU 3.3 0.4 - - - -
657A LEU* 3.7 22.4 - - + -
658A GLY* 2.7 30.5 + - - +
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Residues in contact with VAL 655 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
651A THR* 2.8 32.9 + - + +
652A LEU* 3.8 14.4 - - + +
654A LEU* 1.3 76.7 - - - +
656A GLU* 1.3 62.3 + - - +
658A GLY* 3.2 2.2 + - - -
659A LEU* 3.1 34.3 + - + +
665A LEU* 6.5 0.7 - - + -
668A LEU* 5.4 8.7 - - + -
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Residues in contact with GLU 656 (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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652A LEU 3.1 17.0 + - - +
653A SER* 4.3 7.1 - - - +
655A VAL* 1.3 75.6 - - - +
657A LEU* 1.3 69.1 + - - +
658A GLY 3.6 0.2 + - - -
659A LEU* 3.7 19.5 + - + +
660A ALA 4.2 2.6 + - - -
665A LEU* 5.1 9.7 - - + +
666A SER* 5.7 1.6 + - - -
668A LEU* 3.6 38.1 - - + +
669A ARG* 3.8 30.0 + - - +
672A ARG* 5.9 2.3 + - - -
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Residues in contact with LEU 657 (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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615A LEU* 3.7 30.5 - - + +
618A THR* 4.8 15.3 - - + +
653A SER 3.3 19.2 + - - +
654A LEU* 3.5 22.0 + - + +
655A VAL 3.3 0.2 - - - -
656A GLU* 1.3 84.3 + - - +
658A GLY* 1.3 64.2 + - - +
659A LEU 3.3 1.0 + - - -
660A ALA* 3.7 16.5 + - - +
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Residues in contact with GLY 658 (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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654A LEU* 2.7 23.3 + - - -
655A VAL* 3.2 4.4 + - - -
657A LEU* 1.3 74.2 - - - +
659A LEU* 1.3 66.1 + - - +
660A ALA* 4.8 1.2 - - - +
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Residues in contact with LEU 659 (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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655A VAL* 3.1 22.7 + - + +
656A GLU* 3.9 12.8 - - + +
657A LEU 3.2 0.6 - - - -
658A GLY* 1.3 80.5 - - - +
660A ALA* 1.3 62.6 + - - +
661A ASN* 3.0 27.0 + - - +
662A VAL* 4.6 28.0 - - + +
665A LEU* 3.8 34.8 - - + +
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Residues in contact with ALA 660 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656A GLU 4.2 3.2 + - - -
657A LEU 3.7 16.5 + - - +
658A GLY 4.8 1.3 - - - +
659A LEU* 1.3 78.1 - - - +
661A ASN* 1.3 65.0 + - - +
662A VAL 5.6 0.4 + - - -
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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
------------------------------------------------------------
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