Contacts of the helix formed by residues 2417 - 2422 (chain A) in PDB entry 5ZCS
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 VAL2417 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1900A LEU* 5.9 2.9 - - + -
2197A ARG 4.1 2.7 - - - +
2200A GLN* 3.7 30.7 + - + +
2201A LEU* 3.8 30.3 - - + -
2204A LEU* 3.8 29.8 - - + -
2413A SER 4.1 9.4 + - - +
2414A VAL 4.8 2.9 + - - +
2416A ALA* 1.3 83.5 - - + +
2418A LEU* 1.3 62.3 + - - +
2419A GLU 3.2 5.3 + - - -
2420A ALA* 3.2 20.4 + - - +
2421A PHE* 3.6 10.9 - - + -
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Residues in contact with LEU2418 (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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2362A PHE* 5.6 6.1 - - + -
2414A VAL 3.4 25.1 - - - +
2415A MET* 3.8 10.8 - - - -
2417A VAL* 1.3 77.3 - - - +
2419A GLU* 1.3 82.0 + - + +
2420A ALA 3.2 2.2 + - - -
2421A PHE* 3.6 21.5 - - + -
2422A VAL* 3.3 30.7 - - + +
2423A TYR* 4.8 0.9 - - - -
2500A ILE* 5.4 4.3 - - + -
2501A ILE* 4.6 23.0 - - + +
2504A VAL* 3.8 37.5 - - + -
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Residues in contact with GLU2419 (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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1798A PHE* 6.5 0.4 - - + -
1905A ARG* 4.3 17.5 - - - +
1908A THR* 5.3 9.7 - - + +
1911A PHE* 6.1 0.7 - - - -
1945A ARG* 5.3 1.7 + - - -
2415A MET* 3.0 60.1 - - - +
2416A ALA* 3.4 9.0 + - - +
2417A VAL 3.2 1.2 - - - -
2418A LEU* 1.3 88.9 - - + +
2420A ALA* 1.3 57.5 + - - +
2423A TYR* 3.3 41.6 - - + +
2501A ILE* 5.3 6.8 - - + +
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Residues in contact with ALA2420 (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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1904A LEU* 5.4 9.2 - - + -
1941A GLN* 5.5 11.2 - - + -
1945A ARG* 4.9 3.7 + - - +
2197A ARG* 4.0 9.3 + - - +
2200A GLN* 5.7 5.8 - - - +
2416A ALA 5.2 3.1 - - - +
2417A VAL* 3.2 15.1 + - - +
2419A GLU* 1.3 78.6 - - - +
2421A PHE* 1.3 63.7 + - + +
2422A VAL 3.4 1.1 - - - -
2423A TYR* 3.8 1.9 + - - +
2424A ASP* 3.2 25.2 + - - +
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Residues in contact with PHE2421 (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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2194A GLN* 6.0 4.3 - - + -
2197A ARG* 3.5 54.7 - - + +
2198A VAL* 5.3 7.4 - - + -
2200A GLN* 5.4 0.4 - - - -
2201A LEU* 5.6 2.5 - - + -
2334A LEU* 4.7 19.1 - - + -
2362A PHE* 4.8 13.2 - + - -
2417A VAL* 3.6 18.8 - - + -
2418A LEU* 3.6 28.3 - - + -
2420A ALA* 1.3 77.5 - - + +
2422A VAL* 1.3 72.6 + - + +
2424A ASP* 3.5 12.3 - - - +
2427A LEU* 3.6 19.3 - - + +
2430A ARG* 3.3 38.7 + - - -
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Residues in contact with VAL2422 (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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2362A PHE* 5.7 4.3 - - + -
2418A LEU* 3.3 25.7 + - + +
2420A ALA 3.4 0.6 - - - -
2421A PHE* 1.3 92.1 - - + +
2423A TYR* 1.3 67.5 + - + +
2424A ASP 3.2 0.7 + - - -
2428A ASN* 2.7 33.6 + - - +
2430A ARG* 3.4 22.0 - - - +
2431A LEU* 5.7 3.6 - - + -
2497A ALA* 4.7 22.0 - - + +
2500A ILE* 4.8 27.6 - - + -
2501A ILE* 5.7 5.4 - - + -
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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