Contacts of the strand formed by residues 2434 - 2438 (chain A) in PDB entry 6DLP
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 ILE2434 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2426A TRP* 3.4 35.1 - - + -
2427A ILE 3.4 4.9 - - - +
2428A GLY* 4.8 0.2 - - - -
2433A HIS* 1.3 77.7 - - - +
2435A LEU* 1.3 66.3 + - - +
2446A ARG 4.2 0.3 - - - +
2447A VAL* 3.5 3.1 - - - -
2448A ILE* 2.9 42.6 + - + +
2451A PHE* 3.6 46.2 - - + -
2455A VAL* 3.9 13.2 - - + -
2458A MET* 3.7 29.4 - - + -
2472A VAL* 4.2 7.6 - - + -
2496A TRP* 4.8 4.3 - - + -
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Residues in contact with LEU2435 (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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2387A ILE* 6.3 0.2 - - + -
2389A CYS* 4.2 32.3 - - + +
2392A PHE* 4.1 25.1 - - + -
2393A LEU* 3.6 29.2 - - + -
2425A LEU 3.6 0.8 - - - +
2426A TRP* 3.3 8.5 - - - -
2427A ILE* 2.9 39.5 + - + +
2429A THR* 4.8 6.7 - - + -
2434A ILE* 1.3 78.9 - - - +
2436A LEU* 1.3 61.3 + - - +
2437A LEU* 3.6 20.6 - - + -
2444A LEU* 6.1 0.7 - - + -
2446A ARG 3.7 2.0 - - - +
2447A VAL* 3.7 29.8 - - + -
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Residues in contact with LEU2436 (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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2420A GLN* 4.2 6.5 - - - +
2424A ALA* 3.5 29.2 - - + -
2425A LEU 3.4 10.1 - - - +
2426A TRP* 3.4 56.1 - - + +
2435A LEU* 1.3 74.8 - - - +
2437A LEU* 1.3 61.3 + - - +
2444A LEU* 4.3 0.7 - - - +
2445A ILE* 2.9 39.4 + - + +
2446A ARG* 2.8 39.9 + - + +
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Residues in contact with LEU2437 (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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2387A ILE* 4.0 19.5 - - + -
2392A PHE* 3.8 35.9 - - + -
2424A ALA* 3.3 5.0 - - - -
2425A LEU* 2.9 36.2 + - + +
2427A ILE* 3.7 22.4 - - + -
2435A LEU* 3.6 33.9 - - + -
2436A LEU* 1.3 76.3 - - - +
2438A ASP* 1.3 62.5 + - - +
2439A LEU* 3.6 8.4 - - + +
2443A ARG* 2.9 26.2 - - + +
2444A LEU* 4.4 5.6 - - + -
2445A ILE* 4.0 3.4 - - - -
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Residues in contact with ASP2438 (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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2423A THR* 3.4 24.6 - - - +
2437A LEU* 1.3 75.0 - - - +
2439A LEU* 1.3 79.6 + - - +
2440A SER* 3.4 19.3 + - - -
2441A THR* 4.7 5.4 + - - -
2442A ARG* 2.8 33.4 + - + +
2443A ARG* 2.6 22.9 + - - +
2445A ILE* 3.6 26.9 - - + +
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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