Contacts of the strand formed by residues 2259 - 2265 (chain A) in PDB entry 4ZWJ
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 PRO2259 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2241A SER* 5.2 7.9 - - - -
2242A VAL 4.0 0.7 - - - +
2243A GLU* 4.0 22.9 - - + +
2257A VAL* 6.0 0.2 - - + -
2258A LYS* 1.3 93.9 - - + +
2260A VAL* 1.3 64.3 + - - +
2261A ALA 5.2 1.8 - - - +
2262A SER* 5.6 5.4 - - - +
2288A ASN* 4.2 0.5 - - - +
2291A ARG* 3.5 30.1 + - - +
2294A ILE* 4.4 2.3 - - - +
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Residues in contact with VAL2260 (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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2242A VAL* 2.7 22.4 + - + +
2244A GLN* 3.5 37.0 - - + +
2259A PRO* 1.3 75.5 - - - +
2261A ALA* 1.3 59.4 + - - +
2283A PRO* 4.1 12.1 - - + -
2288A ASN* 2.9 47.2 + - - +
2291A ARG* 4.2 4.0 + - - -
2294A ILE* 5.3 4.0 - - + -
2307A LEU* 3.9 29.2 - - + -
2328A TYR* 4.3 11.2 - - + -
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Residues in contact with ALA2261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2241A SER* 3.4 1.6 - - - -
2242A VAL* 2.7 46.2 + - + +
2259A PRO* 5.2 0.8 - - - +
2260A VAL* 1.3 81.2 + - - +
2262A SER* 1.3 62.7 + - - +
2263A GLU* 6.3 0.4 - - + -
2281A LEU* 4.2 4.3 - - + -
2282A VAL 4.1 11.2 - - - +
2283A PRO* 3.9 29.6 - - + -
2284A LEU 5.4 0.2 - - - +
2288A ASN* 5.4 0.7 - - - +
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Residues in contact with SER2262 (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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2239A LYS* 4.1 23.2 + - - -
2240A VAL 3.4 11.7 - - - -
2241A SER* 4.1 7.2 - - - -
2259A PRO* 5.6 5.8 - - - -
2261A ALA* 1.3 77.6 - - - +
2263A GLU* 1.3 78.6 + - - +
2281A LEU* 4.0 2.0 - - - +
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Residues in contact with GLU2263 (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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2239A LYS* 4.7 0.9 - - - -
2240A VAL* 2.8 34.9 + - - +
2261A ALA* 6.3 0.4 - - + -
2262A SER* 1.3 86.3 + - - +
2264A GLU* 1.3 64.0 + - - +
2279A LEU* 4.3 14.8 - - + +
2280A VAL 4.0 19.5 - - - +
2281A LEU* 3.7 18.2 - - + +
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Residues in contact with GLU2264 (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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2237A LYS* 3.3 38.4 + - + +
2238A ILE 3.4 5.8 - - - +
2239A LYS* 3.6 44.6 + - + +
2263A GLU* 1.3 78.8 + - - +
2265A THR* 1.3 62.9 + - - +
2266A GLN* 4.2 1.9 + - - +
2279A LEU* 4.8 3.4 - - - -
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Residues in contact with THR2265 (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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2237A LYS* 3.4 24.3 - - - +
2238A ILE* 3.0 40.7 + - + +
2264A GLU* 1.3 74.7 - - - +
2266A GLN* 1.3 62.2 + - - +
2267A GLU* 3.5 30.9 + - + +
2275A LEU* 6.1 0.7 - - + -
2277A LYS* 3.9 18.2 + - + +
2279A LEU* 4.3 24.4 - - + +
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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