Contacts of the strand formed by residues 240 - 245 (chain 1) in PDB entry 3EPD
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 VAL 240 (chain 1).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1071 MET* 3.5 30.7 - - + -
1081 TRP 3.1 10.1 - - - +
1091 ARG* 3.6 36.6 - - + +
1101 ILE* 4.3 3.1 - - - -
1591 TYR* 3.5 5.4 - - - -
1601 ILE* 2.9 47.0 + - + +
1661 THR* 4.6 2.0 - - + -
2391 GLY* 1.3 80.1 - - - +
2411 LEU* 1.3 64.1 + - - +
126R VAL* 4.7 2.0 - - + -
127R THR 4.7 0.9 - - - +
132R SER* 3.5 19.1 - - - +
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Residues in contact with LEU 241 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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901 ILE* 5.0 0.7 - - + -
1061 ALA 3.8 0.7 - - - +
1071 MET* 3.2 3.9 - - - -
1081 TRP* 2.9 49.4 + - + +
1101 ILE* 4.0 17.9 - - + +
1341 PHE* 5.1 6.1 - - + -
1361 PHE* 4.1 17.7 - - + -
1571 ILE* 4.3 13.9 - - + -
1581 MET 3.5 3.1 - - - +
1591 TYR* 4.0 20.4 - - - -
2401 VAL* 1.3 74.2 - - - +
2421 ALA* 1.3 58.9 + - - +
2431 VAL* 4.1 7.6 + - + +
2601 ILE* 3.7 29.6 - - + -
10001 SPH 4.0 27.8 - - + -
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Residues in contact with ALA 242 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1051 PHE* 5.2 0.2 - - + -
1061 ALA 3.3 7.2 - - - +
1071 MET* 3.8 13.0 - - + -
1561 GLN 3.6 1.4 - - - +
1571 ILE* 3.5 1.6 - - - -
1581 MET* 2.9 36.1 + - + +
1601 ILE* 3.7 26.5 - - + -
1671 PRO* 4.2 3.8 - - + -
1751 TRP* 3.6 24.4 - - + -
2401 VAL 4.0 1.0 + - - -
2411 LEU* 1.3 71.6 - - - +
2431 VAL* 1.3 59.2 + - - +
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Residues in contact with VAL 243 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
901 ILE* 4.1 35.0 - - + -
921 VAL* 3.9 17.2 - - + +
1051 PHE* 3.1 5.5 - - - +
1061 ALA* 2.9 34.7 + - + +
1551 TYR* 4.9 4.7 - - + -
1561 GLN 3.3 9.0 - - - +
1571 ILE* 4.3 24.7 - - + -
1751 TRP* 4.1 1.3 - - - -
2411 LEU* 4.7 4.5 - - + +
2421 ALA* 1.3 77.3 - - - +
2441 ARG* 1.3 65.8 + - - +
2581 VAL* 4.0 26.5 - - + -
2601 ILE* 6.2 0.2 - - + -
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Residues in contact with ARG 244 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921 VAL* 4.0 4.9 - - - -
1041 LEU 3.8 16.4 - - - +
1051 PHE* 4.0 3.6 - - + -
1551 TYR* 3.4 7.2 - - - +
1561 GLN* 2.9 60.7 + - + +
1701 TRP* 2.8 50.1 + - + +
1711 ASP* 2.9 28.5 + - - +
1751 TRP* 3.7 39.2 + - + +
1841 PHE* 5.0 2.4 - - - -
2431 VAL* 1.3 77.6 - - - +
2451 VAL* 1.3 65.2 + - - +
2461 VAL* 4.1 22.2 + - - +
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Residues in contact with VAL 245 (chain 1).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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921 VAL* 4.3 10.9 - - + +
931 ASP 4.3 11.4 - - - +
941 ASN* 4.0 25.0 + - + +
1041 LEU 4.2 4.7 + - - +
1531 GLN* 3.8 33.9 - - + +
1541 VAL 3.7 7.0 - - - +
1551 TYR* 3.8 26.0 - - + +
1701 TRP* 3.5 21.1 - - - -
2441 ARG* 1.3 75.0 - - - +
2461 VAL* 1.3 62.1 + - - +
2471 ASN* 3.6 20.1 + - + +
2561 SER* 4.8 2.0 - - - +
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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