Contacts of the strand formed by residues 126 - 131 (chain 5) in PDB entry 1G6Q
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 126 (chain 5).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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615 ILE* 3.5 24.2 - - + +
625 VAL* 3.8 1.8 - - - -
635 LEU* 3.4 33.9 - - + +
855 ILE* 4.9 4.7 - - + -
1215 LEU* 4.9 2.0 - - + -
1235 PHE 3.8 10.8 - - - +
1255 LYS* 1.3 71.7 - - - +
1275 ASP* 1.3 63.2 + - - +
1285 ILE 3.1 29.4 - - - +
1295 ILE* 4.8 2.7 - - + -
1545 TYR* 2.8 31.8 + - + +
1555 LEU* 3.4 6.1 - - + +
1565 VAL* 3.0 24.9 + - - +
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Residues in contact with ASP 127 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605 LYS* 3.1 33.8 - - + +
615 ILE* 3.0 39.5 + - - +
1255 LYS 4.1 3.5 - - - +
1265 VAL* 1.3 73.4 - - - +
1285 ILE* 1.3 62.6 + - + +
1555 LEU* 3.9 2.0 - - - -
1565 VAL* 3.7 21.3 - - + +
1595 GLY* 3.2 26.2 - - - -
1605 LEU 3.2 3.6 + - - -
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Residues in contact with ILE 128 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565 LEU* 3.8 27.1 - - + +
575 PHE* 3.7 47.8 - - + -
605 LYS* 3.9 11.2 - - + -
615 ILE 3.2 2.7 + - - +
625 VAL* 3.0 17.4 - - + +
635 LEU 2.8 23.6 + - - -
1265 VAL* 3.1 4.2 - - - +
1275 ASP* 1.3 88.1 - - + +
1295 ILE* 1.3 64.0 + - - +
1305 ILE* 4.3 1.6 - - + -
1555 LEU* 4.4 0.2 - - - -
1605 LEU* 3.5 28.0 - - + +
1625 PHE* 3.7 16.6 - - + -
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Residues in contact with ILE 129 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635 LEU* 3.3 23.3 - - + +
655 VAL* 4.0 14.4 - - + -
1265 VAL* 4.8 1.6 - - + -
1285 ILE* 1.3 74.7 - - - +
1305 ILE* 1.3 64.3 + - - +
1475 VAL* 4.1 14.1 - - + +
1505 ALA* 3.3 35.4 - - + +
1515 ARG* 4.1 10.1 - - + +
1555 LEU* 3.5 28.0 - - + -
1605 LEU 2.8 11.0 + - - +
1615 ILE* 3.3 23.0 - - + +
1625 PHE 2.8 23.7 + - - -
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Residues in contact with ILE 130 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465 TYR* 5.3 2.0 - - + -
505 ILE* 4.4 18.6 - - + -
575 PHE* 4.6 2.0 - - + -
625 VAL* 4.1 22.0 - - + -
635 LEU 2.8 10.9 + - - +
645 ASP* 3.1 36.8 - - + +
655 VAL* 2.7 25.8 + - - +
725 LEU* 3.6 32.5 - - + +
735 SER* 4.1 3.4 - - - +
765 ALA* 4.8 3.6 - - + -
845 VAL* 5.4 0.2 - - + -
1285 ILE* 4.3 2.7 - - + -
1295 ILE* 1.3 79.4 - - - +
1315 SER* 1.3 61.9 + - - +
1625 PHE* 3.6 33.9 - - + +
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Residues in contact with SER 131 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465 TYR* 2.9 19.9 + - - -
645 ASP* 4.5 2.0 - - - -
655 VAL* 3.1 31.2 + - - +
725 LEU* 4.5 1.8 - - - +
1305 ILE* 1.3 77.7 - - - +
1325 GLU* 1.3 61.3 + - - +
1335 TRP* 3.2 26.4 + - - +
1435 MET* 4.8 1.2 - - - +
1475 VAL* 3.3 27.6 - - - +
1615 ILE* 6.0 0.8 - - - +
1625 PHE 3.0 14.4 + - - +
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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