Contacts of the strand formed by residues 2710 - 2713 (chain G) in PDB entry 2ZLE
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 LEU2710 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2675G ILE* 5.7 5.2 - - + -
2677G LEU* 5.5 6.7 - - + -
2683G ILE* 4.8 13.2 - - + -
2687G ASN* 4.8 5.8 - - + +
2697G LEU* 4.7 13.7 - - + -
2701G LEU* 4.5 11.7 - - + -
2708G LEU* 3.4 36.1 - - + -
2709G ALA* 1.3 68.5 - - - +
2711G ASN* 1.3 52.5 + - - +
2712G ILE* 2.5 39.6 + - + +
2719G ILE 3.5 8.3 - - - +
2720G TYR* 3.6 8.1 - - - -
2721G LEU* 2.7 18.5 + - + +
2722G LEU 3.0 29.8 - - - +
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Residues in contact with ASN2711 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2683G ILE* 4.8 1.1 - - - -
2684G ILE 3.9 1.2 + - - -
2685G GLY* 3.2 33.5 + - - +
2687G ASN* 3.1 15.6 + - - -
2688G GLN* 3.6 22.7 + - - +
2709G ALA* 2.7 17.2 - - - +
2710G LEU* 1.3 65.6 - - - +
2712G ILE* 1.3 53.8 + - - +
2713G GLN* 2.6 34.5 + - - +
2719G ILE 4.0 0.2 - - - -
2720G TYR* 3.7 30.5 - - + -
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Residues in contact with ILE2712 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2676G GLY 3.4 14.6 - - - +
2677G LEU* 3.4 31.4 - - + -
2681G ASP* 3.7 19.3 - - + +
2682G VAL 3.2 14.1 - - - +
2683G ILE* 3.5 23.1 - - + +
2710G LEU* 2.5 39.5 + - + +
2711G ASN* 1.3 74.0 - - - +
2713G GLN* 1.3 61.7 + - - +
2714G ARG* 5.1 1.3 - - + +
2717G SER 3.8 0.2 - - - +
2718G THR* 3.5 2.3 - - - -
2719G ILE* 2.9 41.2 + - + +
2721G LEU* 4.3 2.9 - - + -
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Residues in contact with GLN2713 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2682G VAL* 3.0 24.6 + - + +
2683G ILE* 3.9 1.4 - - - +
2684G ILE* 3.0 43.5 - - + +
2685G GLY 3.8 0.8 - - - +
2711G ASN* 2.6 31.1 + - - +
2712G ILE* 1.3 72.7 - - - +
2714G ARG* 1.3 58.1 + - - +
2715G GLY 2.8 15.6 + - - +
2716G ASP 4.7 1.8 - - - +
2717G SER 2.9 14.8 - - - +
2718G THR* 3.2 33.7 - - + +
2720G TYR* 5.1 0.2 - - - -
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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