Contacts of the helix formed by residues 60 - 72 (chain 7) in PDB entry 6AH0
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 60 (chain 7).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3063 GLU* 6.0 7.0 - - - +
547 ALA* 5.1 7.6 - - - -
597 GLU* 1.3 78.8 - - - +
617 LYS* 1.3 69.6 + - - +
627 ALA 3.1 4.5 - - - +
637 ARG* 4.1 9.0 - - - +
647 VAL* 3.3 12.8 + - - -
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Residues in contact with LYS 61 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547 ALA* 5.8 4.2 - - - +
597 GLU 4.0 0.2 + - - -
607 SER* 1.3 72.1 - - - +
627 ALA* 1.3 67.5 - - - +
647 VAL* 3.0 5.5 + - - -
657 ARG* 2.9 14.6 + - - -
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Residues in contact with ALA 62 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2883 VAL* 6.2 4.0 - - - +
607 SER* 3.1 2.4 - - - +
617 LYS* 1.3 73.9 - - - +
637 ARG* 1.3 54.1 + - - +
657 ARG* 2.5 28.4 + - - +
667 PHE* 2.8 11.6 + - - -
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Residues in contact with ARG 63 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 GLU* 6.1 0.4 - - - +
607 SER* 3.7 12.1 + - - +
617 LYS 3.5 0.6 - - - -
627 ALA* 1.3 72.0 - - - +
647 VAL* 1.3 64.8 + - - +
667 PHE* 3.9 2.7 - - - +
677 ASN* 2.9 18.2 + - - -
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Residues in contact with VAL 64 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
597 GLU* 5.9 0.4 - - - +
607 SER 3.3 10.2 + - - +
617 LYS 3.0 7.9 + - - -
627 ALA 2.7 4.4 + - - -
637 ARG* 1.3 79.3 - - - +
657 ARG* 1.3 64.9 + - - +
677 ASN* 2.8 9.0 + - - -
687 LEU* 2.9 10.4 + - - -
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Residues in contact with ARG 65 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447 MET* 6.5 1.6 - - - +
617 LYS 2.9 8.0 + - - -
627 ALA* 2.5 11.5 + - - +
647 VAL* 1.3 70.1 - - - +
667 PHE* 1.3 61.2 + - - +
687 LEU* 3.1 3.1 + - - +
697 MET* 2.9 20.4 + - - -
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Residues in contact with PHE 66 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2333 ASN* 6.5 0.9 - - - +
627 ALA 2.8 17.0 + - - -
637 ARG* 3.9 3.1 - - - +
647 VAL 2.9 0.4 + - - -
657 ARG* 1.3 69.3 - - - +
677 ASN* 1.3 63.5 + - - +
697 MET* 2.9 14.6 + - - +
707 GLU 2.9 9.4 + - - -
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Residues in contact with ASN 67 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637 ARG 2.9 12.4 + - - -
647 VAL 2.8 11.7 + - - -
667 PHE* 1.3 69.5 - - - +
687 LEU* 1.3 62.5 + - - +
707 GLU* 2.8 13.0 + - - +
717 LYS* 2.9 10.7 + - - -
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Residues in contact with LEU 68 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647 VAL 2.9 12.0 + - - -
657 ARG* 3.5 4.0 - - - +
677 ASN* 1.3 74.2 - - - +
697 MET* 1.3 54.7 + - - +
717 LYS* 2.6 25.9 + - - +
727 MET* 2.9 11.1 + - - -
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Residues in contact with MET 69 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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657 ARG 2.9 9.8 + - - -
667 PHE* 2.9 8.9 + - - +
687 LEU* 1.3 75.5 - - - +
707 GLU* 1.3 60.3 + - - +
727 MET* 4.1 6.8 + - - +
737 LEU 5.3 0.3 + - - -
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Residues in contact with GLU 70 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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667 PHE 2.9 7.8 + - - -
677 ASN* 2.8 10.8 + - - +
697 MET* 1.3 77.0 - - - +
717 LYS* 1.3 57.0 + - - +
727 MET 2.9 9.8 + - - -
737 LEU 3.9 6.4 + - - -
747 GLN* 4.5 2.8 + - - -
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Residues in contact with LYS 71 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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677 ASN 2.9 7.7 + - - -
687 LEU* 2.6 15.1 + - - +
707 GLU* 1.3 70.3 - - - +
727 MET* 1.3 62.6 + - - +
737 LEU 3.5 0.4 - - - -
747 GLN* 3.4 3.5 + - - +
757 PRO* 3.3 22.8 - - - +
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Residues in contact with MET 72 (chain 7).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377 ARG* 5.2 13.4 + - - +
687 LEU 2.9 12.2 + - - -
697 MET* 4.1 5.6 - - - +
707 GLU 2.9 4.9 + - - -
717 LYS* 1.3 77.8 - - - +
737 LEU* 1.3 61.1 + - - +
757 PRO 4.2 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