Contacts of the helix formed by residues 686 - 697 (chain B) in PDB entry 4MNE
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 PRO 686 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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550B MET* 3.6 18.2 - - + -
554B ILE* 3.9 24.2 - - + -
684B ASN 3.2 10.9 - - - +
685B CYS* 1.3 88.7 - - + +
687B LYS* 1.3 65.7 + - - +
688B ALA 4.2 0.7 - - - +
689B MET* 3.0 26.8 + - + +
690B LYS 3.3 8.7 + - - -
717B LEU* 4.1 22.2 - - + -
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Residues in contact with LYS 687 (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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685B CYS 3.4 4.8 + - - +
686B PRO* 1.3 70.8 - - - +
688B ALA* 1.3 57.5 + - - +
690B LYS* 3.4 8.1 + - - +
691B ARG* 3.0 28.4 + - - +
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Residues in contact with ALA 688 (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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686B PRO* 3.1 1.0 - - - +
687B LYS* 1.3 78.4 - - - +
689B MET* 1.3 58.4 + - - +
691B ARG* 3.6 8.3 + - - +
692B LEU* 2.9 28.9 + - - +
713B SER* 5.5 2.6 - - - +
717B LEU* 3.8 34.8 - - + -
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Residues in contact with MET 689 (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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554B ILE* 4.6 24.0 - - + -
557B ALA* 4.6 6.7 - - + -
646B LEU* 3.5 35.4 - - + -
650B MET* 3.9 20.0 - - + -
685B CYS* 3.7 12.8 - - - -
686B PRO* 3.0 32.8 + - + +
688B ALA* 1.3 76.4 - - - +
690B LYS* 1.3 56.3 + - - +
692B LEU* 3.1 16.8 + - + +
693B MET* 2.7 39.3 + - - +
714B ILE* 4.8 9.4 - - + -
717B LEU* 4.8 9.4 - - + -
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Residues in contact with LYS 690 (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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678B LEU* 3.3 44.9 + - + +
679B SER* 4.4 6.1 - - - +
681B VAL* 3.7 24.2 - - + +
685B CYS* 3.8 11.5 - - - +
686B PRO 3.3 7.2 + - - +
687B LYS* 3.7 11.0 - - - +
689B MET* 1.3 77.3 - - - +
691B ARG* 1.3 63.5 - - - +
693B MET* 3.5 9.8 - - + +
694B ALA* 3.0 23.0 + - + +
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Residues in contact with ARG 691 (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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687B LYS 3.0 16.7 + - - +
688B ALA* 3.7 7.9 - - - +
690B LYS* 1.3 75.8 - - - +
692B LEU* 1.3 59.0 + - - +
694B ALA* 3.2 7.2 + - - +
695B GLU* 2.9 57.9 + - + +
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Residues in contact with LEU 692 (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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646B LEU* 4.1 16.8 - - + -
688B ALA 2.9 19.6 + - - +
689B MET* 3.5 14.4 - - + +
691B ARG* 1.3 76.6 - - - +
693B MET* 1.3 62.3 + - - +
695B GLU* 3.3 9.9 + - - +
696B CYS* 3.0 27.0 + - - -
705B PRO* 4.6 9.0 - - + -
709B GLN* 6.3 0.2 - - - +
710B ILE* 4.1 30.1 - - + -
713B SER* 3.9 27.4 - - - +
714B ILE* 3.9 29.6 - - + -
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Residues in contact with MET 693 (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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643B GLY 3.9 17.0 - - - +
646B LEU* 3.6 28.7 - - + +
647B TYR* 3.8 19.3 - - - -
650B MET* 3.5 37.2 - - + -
678B LEU* 3.9 21.8 - - + -
681B VAL* 3.9 16.2 - - + -
689B MET 2.7 19.9 + - - +
690B LYS* 3.5 7.0 - - - +
692B LEU* 1.3 74.4 - - - +
694B ALA* 1.3 62.3 + - - +
696B CYS* 3.1 3.7 + - - +
697B LEU* 3.1 35.3 + - + +
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Residues in contact with ALA 694 (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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678B LEU* 3.5 29.8 - - + +
690B LYS* 3.0 12.2 + - + +
691B ARG* 3.2 10.5 + - - +
693B MET* 1.3 76.2 - - - +
695B GLU* 1.3 62.0 + - + +
697B LEU* 3.4 7.2 + - - +
698B LYS* 3.4 28.8 + - - +
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Residues in contact with GLU 695 (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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691B ARG* 2.9 55.4 + - + +
692B LEU* 3.7 10.9 - - - +
693B MET 3.1 0.2 - - - -
694B ALA* 1.3 76.2 - - + +
696B CYS* 1.3 65.8 + - - +
697B LEU 3.0 2.7 + - - -
698B LYS* 3.3 36.1 + - + +
703B GLU 5.2 2.5 - - - +
704B ARG* 3.7 3.5 - - - -
705B PRO* 3.6 31.2 - - + +
709B GLN* 4.4 11.4 + - - -
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Residues in contact with CYS 696 (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 VAL* 3.7 16.4 - - + +
640B TYR* 3.4 13.7 + - - -
642B PHE* 4.1 14.4 - - - -
643B GLY* 3.7 21.3 - - - -
646B LEU* 4.4 1.6 - - - -
692B LEU* 3.0 26.2 + - - +
693B MET* 3.1 2.0 + - - +
695B GLU* 1.3 76.5 - - - +
697B LEU* 1.3 58.6 + - - +
698B LYS 3.4 0.2 - - - -
704B ARG* 3.3 22.1 - - - -
705B PRO* 4.1 9.0 - - - -
710B ILE* 3.7 31.6 - - - -
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Residues in contact with LEU 697 (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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640B TYR* 3.6 33.3 - - + +
643B GLY 3.8 19.5 - - - +
644B ILE* 3.6 28.5 - - + +
647B TYR* 4.8 1.8 - - + -
676B PRO* 3.9 26.4 - - + +
678B LEU* 4.0 15.5 - - + -
693B MET* 3.1 34.7 + - + +
694B ALA* 3.8 7.6 - - - +
695B GLU 3.0 1.2 - - - -
696B CYS* 1.3 78.1 - - - +
698B LYS* 1.3 67.3 + - - +
699B LYS* 3.4 5.7 + - - +
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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