Contacts of the strand formed by residues 2525 - 2529 (chain B) in PDB entry 2H7C
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 GLY2525 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446B MET 4.8 1.0 + - - -
2518B PRO* 3.9 22.1 - - - +
2519B GLU 3.8 9.8 + - - +
2520B TYR* 3.4 25.1 - - - +
2521B ASN* 4.6 1.4 + - - -
2523B LYS* 3.3 3.2 - - - +
2524B GLU* 1.3 79.2 - - - +
2526B TYR* 1.3 59.3 + - - -
2536B ALA 3.2 12.1 - - - -
2537B GLN* 4.1 9.0 - - - -
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Residues in contact with TYR2526 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2446B MET* 3.4 29.2 - - + +
2448B GLU* 4.0 18.7 + - + -
2517B TRP* 4.4 4.5 - - - +
2518B PRO* 3.9 5.3 - - - +
2520B TYR* 4.9 1.6 - - + -
2524B GLU 3.9 5.2 - - - +
2525B GLY* 1.3 73.3 - - - +
2527B LEU* 1.3 69.0 + - - +
2528B GLN* 3.4 33.6 + - + -
2535B ALA* 3.4 4.6 - - - +
2536B ALA* 2.9 43.8 + - + +
2537B GLN 3.5 21.7 + - - -
2538B LYS 5.3 0.2 - - - -
2539B LEU* 3.5 60.2 - - + +
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Residues in contact with LEU2527 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2446B MET 3.0 7.9 + - - -
2447B TYR* 3.1 5.7 - - - +
2448B GLU 2.9 26.0 + - - -
2499B PHE* 3.4 35.2 - - + -
2515B PRO* 4.9 2.9 - - + -
2516B HIS 3.8 17.7 - - - +
2517B TRP* 3.5 39.6 - - + +
2526B TYR* 1.3 76.8 - - - +
2528B GLN* 1.3 58.9 + - - +
2529B ILE* 3.7 12.3 - - + -
2533B THR* 3.8 21.3 - - + -
2534B GLN* 3.6 26.2 - - - -
2535B ALA* 3.8 4.7 - - - +
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Residues in contact with GLN2528 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2352B LYS* 5.9 2.2 - - - +
2448B GLU* 3.6 14.3 + - + +
2526B TYR* 3.4 34.5 + - + -
2527B LEU* 1.3 69.9 - - - +
2529B ILE* 1.3 61.1 + - - +
2532B ASN 3.9 3.1 - - - +
2533B THR* 3.1 8.7 - - - +
2534B GLN* 2.9 67.6 + - + +
2536B ALA* 3.8 16.9 - - + +
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Residues in contact with ILE2529 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2447B TYR* 3.8 29.6 - - + -
2448B GLU 2.9 11.1 + - - +
2449B PHE* 3.5 26.4 - - + -
2450B GLN* 2.8 30.0 + - - +
2492B LEU* 4.0 8.5 - - + -
2495B MET* 3.8 20.9 - - + -
2496B VAL* 4.1 7.2 - - + -
2499B PHE* 5.0 4.3 - - + -
2500B TRP* 4.2 23.1 - - + -
2517B TRP* 4.3 2.2 - - + -
2527B LEU* 3.9 31.0 - - + +
2528B GLN* 1.3 74.4 - - - +
2530B GLY* 1.3 61.6 + - - +
2532B ASN 5.1 0.4 - - - -
2533B THR* 3.8 3.8 - - + -
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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