Contacts of the helix formed by residues 671 - 681 (chain S) in PDB entry 4US2
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 671 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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670S LEU 1.3 67.9 + - - +
672S ALA* 1.4 63.0 + - - +
673S GLU* 4.0 7.4 + - - +
674S LEU* 3.6 23.8 + - - +
675S LYS* 3.2 23.7 + - - +
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Residues in contact with ALA 672 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671S SER* 1.4 71.3 - - - +
673S GLU* 1.4 64.2 + - - +
675S LYS* 3.6 6.2 + - - +
676S ARG* 3.2 25.5 + - - +
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Residues in contact with GLU 673 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567S MET* 5.5 0.2 - - - +
568S ARG* 6.3 4.7 - - + +
671S SER* 3.4 8.1 + - - +
672S ALA* 1.4 79.5 - - - +
674S LEU* 1.4 56.6 + - - +
676S ARG* 3.7 13.0 + - - +
677S PHE* 3.1 26.2 + - - +
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Residues in contact with LEU 674 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652S GLU* 6.1 4.7 - - + -
653S PRO* 6.0 4.5 - - + -
670S LEU 5.5 0.7 - - - -
671S SER* 3.6 21.6 + - - +
672S ALA 3.4 0.6 - - - -
673S GLU* 1.4 77.0 - - - +
675S LYS* 1.4 58.1 + - - +
677S PHE* 3.2 7.5 + - - +
678S ARG* 2.9 51.9 + - - +
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Residues in contact with LYS 675 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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671S SER 3.2 18.3 + - - +
672S ALA* 4.0 7.0 - - - +
673S GLU 3.5 0.2 - - - -
674S LEU* 1.4 74.9 - - - +
676S ARG* 1.3 59.9 + - - +
678S ARG* 3.9 9.6 + - - +
679S LYS* 3.4 22.5 + - - +
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Residues in contact with ARG 676 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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566S GLN* 3.8 12.9 + - - +
567S MET* 3.4 47.8 - - + +
568S ARG 5.4 0.2 - - - +
672S ALA 3.2 17.8 + - - +
673S GLU* 3.9 13.4 + - - +
675S LYS* 1.3 72.6 - - - +
677S PHE* 1.4 56.9 + - - +
679S LYS* 3.3 3.5 + - - -
680S GLU* 2.7 67.1 + - + +
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Residues in contact with PHE 677 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567S MET* 3.4 20.6 - - + +
568S ARG 3.7 24.2 - - - -
569S LEU* 3.8 22.4 - - + -
570S PRO* 3.8 20.4 - - + -
650S ILE* 4.1 2.7 - - + -
651S PRO 3.8 14.4 - - - -
652S GLU* 4.4 2.9 - - + -
653S PRO* 4.0 17.5 - - + -
673S GLU 3.1 20.5 + - - +
674S LEU* 3.2 8.7 + - - +
676S ARG* 1.4 75.4 - - - +
678S ARG* 1.3 57.0 + - + +
681S TYR* 2.8 48.5 + + + +
682S ILE* 3.1 38.1 + - + -
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Residues in contact with ARG 678 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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652S GLU* 6.4 2.0 - - - -
674S LEU* 2.9 36.4 + - - +
675S LYS* 4.2 7.4 - - - +
676S ARG 3.4 0.2 - - - -
677S PHE* 1.3 75.5 - - + +
679S LYS* 1.4 56.6 + - - +
682S ILE* 3.9 27.7 - - + +
683S GLN* 3.1 30.5 + - - +
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Residues in contact with LYS 679 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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675S LYS 3.4 15.1 + - - +
676S ARG* 3.3 5.2 + - - +
677S PHE 3.3 0.4 - - - -
678S ARG* 1.4 79.4 - - - +
680S GLU* 1.4 63.7 + - + +
681S TYR 3.7 0.4 - - - -
683S GLN* 4.5 7.7 + - - +
684S PRO* 3.4 17.2 - - - +
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Residues in contact with GLU 680 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567S MET* 3.8 14.0 - - - +
616S HIS* 3.4 25.8 - - - +
676S ARG* 2.7 57.1 + - + +
679S LYS* 1.4 77.0 - - + +
681S TYR* 1.3 58.1 + - - +
684S PRO* 3.8 9.8 - - - +
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Residues in contact with TYR 681 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567S MET* 4.1 4.9 - - + -
569S LEU* 3.6 32.8 - - + +
570S PRO* 5.7 1.1 - - + -
575S TYR* 4.0 15.8 - + - -
577S PHE 4.0 10.4 + - - -
578S ALA* 5.0 0.9 - - - -
611S GLU* 5.2 1.7 - - - +
616S HIS* 3.5 41.5 - + + -
647S ARG* 3.1 31.4 + - - -
650S ILE* 4.1 20.2 - - + -
677S PHE* 2.8 47.6 + + + +
679S LYS 3.7 0.6 - - - -
680S GLU* 1.3 73.4 - - - +
682S ILE* 1.3 66.3 + - - +
683S GLN 3.6 0.9 - - - -
684S PRO* 3.5 2.2 - - - +
685S VAL* 3.1 31.8 + - + +
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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