Contacts of the strand formed by residues 239 - 242 (chain 4) in PDB entry 3EXG
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 ARG 239 (chain 4).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1454 VAL* 3.4 2.1 - - - +
1464 SER* 2.6 47.6 + - - +
1514 GLU* 4.3 6.5 + - - -
1524 ASP* 2.8 32.5 + - - +
1564 LEU* 4.3 16.2 - - + -
1934 ILE* 3.4 42.4 - - - +
1944 PRO* 5.6 1.0 - - - +
1974 LYS* 3.6 21.3 + - - +
1984 ALA 4.2 3.4 + - - -
1994 LYS* 2.9 51.9 - - - +
2114 SER 4.8 0.2 + - - -
2124 HIS* 4.9 0.8 - - - +
2374 ASN* 3.0 19.7 + - - +
2384 MET* 1.3 75.8 - - - +
2404 THR* 1.3 60.0 + - - +
2414 ILE* 3.8 0.4 + - - -
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Residues in contact with THR 240 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1444 VAL 3.5 5.4 - - - +
1454 VAL* 4.0 5.9 - - + +
1564 LEU* 5.2 1.9 - - - +
1944 PRO 4.8 0.3 + - - -
1954 ILE* 3.7 14.1 - - + +
1964 GLY* 2.8 35.7 + - - +
1974 LYS 4.1 2.0 + - - -
2384 MET* 2.7 24.9 + - - +
2394 ARG* 1.3 77.7 - - - +
2414 ILE* 1.3 63.0 - - - +
2424 ARG 3.4 29.8 - - - +
2434 PRO* 3.5 15.9 - - + +
2444 MET* 3.7 15.1 - - - +
2454 ASP 4.7 1.5 + - - -
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Residues in contact with ILE 241 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1334 ALA* 3.9 31.2 - - + +
1374 GLY* 4.4 2.2 - - - -
1444 VAL* 2.6 34.2 + - + +
1464 SER* 3.9 27.8 - - - -
2124 HIS* 4.0 26.5 - - + +
2384 MET* 4.8 7.4 - - + -
2394 ARG 4.7 0.4 - - - +
2404 THR* 1.3 77.7 - - - +
2424 ARG* 1.3 59.1 + - - +
2444 MET* 3.3 30.1 + - + +
2714 VAL* 4.7 4.9 - - + -
2686 GLN* 5.4 0.3 - - - +
2696 PHE* 3.8 28.4 - - + -
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Residues in contact with ARG 242 (chain 4).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3403 TYR* 4.0 11.3 + - - +
1364 TYR 4.7 1.1 - - - -
1374 GLY* 2.9 39.5 + - - +
1384 HIS 3.7 13.3 + - - -
1394 CYS 3.4 15.9 + - - -
1404 PRO* 3.2 29.5 - - - +
1424 LEU 3.7 12.1 - - - +
1434 LYS* 3.3 9.8 - - - +
1444 VAL 2.9 36.9 + - - +
2404 THR* 3.4 5.6 - - - +
2414 ILE* 1.3 80.1 - - - +
2434 PRO* 1.3 68.8 - - + +
2686 GLN* 3.0 31.0 - - - +
2696 PHE* 5.2 0.2 - - + -
2996 ASP* 2.7 33.3 + - - -
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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