Contacts of the helix formed by residues 637 - 643 (chain A) in PDB entry 5N4D
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 637 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589A ARG* 3.3 19.5 + - - +
633A ASP 3.3 26.2 - - - +
634A TYR* 3.6 8.3 - - - +
635A ILE 3.4 4.5 - - - -
636A TYR* 1.3 94.1 - - + +
638A LEU* 1.3 58.3 + - + +
643A ASN* 3.3 22.2 + - - +
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Residues in contact with LEU 638 (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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543A ARG 5.6 0.2 - - - +
546A LYS* 3.8 17.7 - - + -
547A VAL* 3.6 41.7 - - + +
550A PHE* 3.9 21.5 - - + -
585A GLY* 5.0 5.0 - - - -
589A ARG* 3.3 42.7 - - - +
607A LEU* 4.3 13.4 - - + +
634A TYR 4.0 14.1 - - - +
635A ILE* 2.9 10.3 + - - +
637A PRO* 1.3 80.0 - - + +
639A SER* 1.3 64.9 + - - +
640A PRO* 3.1 12.6 - - - +
643A ASN* 4.0 1.5 - - - +
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Residues in contact with SER 639 (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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605A ALA 3.5 2.8 + - - -
607A LEU* 3.0 38.6 + - - -
608A LEU* 4.7 1.3 - - - -
635A ILE 3.1 7.0 + - - -
636A TYR* 3.3 15.0 + - - -
638A LEU* 1.3 75.3 - - - +
640A PRO* 1.3 69.5 - - - +
642A HIS* 2.7 35.7 + - - -
643A ASN* 2.8 20.7 + - - -
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Residues in contact with PRO 640 (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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581A LEU* 3.6 30.7 - - + -
584A MET* 4.1 6.5 - - + +
585A GLY* 3.7 29.2 - - - +
588A VAL* 4.0 8.6 - - + +
605A ALA* 3.2 19.7 - - + +
607A LEU* 4.4 2.5 - - + -
638A LEU 3.1 7.6 - - - +
639A SER* 1.3 82.2 - - - +
641A VAL* 1.3 60.7 + - - +
642A HIS 3.1 0.9 + - - -
643A ASN* 3.2 11.7 + - + +
644A VAL* 3.5 17.8 + - - +
672A PHE* 3.6 24.2 - - + -
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Residues in contact with VAL 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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35A ASP* 5.0 4.7 - - - +
605A ALA* 3.1 37.7 + - + +
606A ASP* 3.8 6.3 - - + +
639A SER 3.3 0.4 - - - -
640A PRO* 1.3 74.8 - - - +
642A HIS* 1.3 80.9 + - + +
643A ASN 3.4 0.6 + - - -
644A VAL* 4.6 2.1 + - - -
668A HIS 4.3 0.7 - - - +
671A LYS* 4.2 22.0 - - + -
672A PHE* 3.9 26.2 - - + +
675A THR* 3.8 31.0 - - - +
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Residues in contact with HIS 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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33A VAL* 3.7 26.9 - - + +
34A PRO 5.0 3.8 - - - -
35A ASP* 4.8 7.6 + - - -
606A ASP* 3.4 32.1 + - - -
608A LEU* 3.6 25.8 - - + +
636A TYR* 3.9 21.1 + + + +
639A SER* 2.7 32.2 + - - +
641A VAL* 1.3 92.1 - - + +
643A ASN* 1.3 70.9 + - - +
644A VAL 3.7 1.3 - - - -
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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
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588A VAL* 3.1 33.2 - - + +
589A ARG* 6.3 0.7 - - + -
636A TYR 2.9 24.5 + - - +
637A PRO* 3.3 26.8 + - - +
638A LEU 4.0 0.6 - - - -
639A SER 2.8 24.0 + - - +
640A PRO 3.2 2.6 + - - -
642A HIS* 1.3 84.9 + - - +
644A VAL* 1.3 66.2 + - - +
645A ARG* 3.5 11.5 + - - +
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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