Contacts of the strand formed by residues 974 - 979 (chain A) in PDB entry 3F2B
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 ILE 974 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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872A ILE* 3.7 38.5 - - + +
873A TYR* 3.8 20.2 - - + -
876A SER* 3.4 31.4 - - - +
896A VAL* 3.7 31.6 - - + -
907A ILE* 4.5 7.6 - - + -
963A PHE* 4.6 3.8 - - + -
973A ASP* 1.3 79.5 - - - +
975A ASP* 1.3 64.4 + - - +
976A LEU* 4.0 14.7 + - + +
1096A LYS 3.7 4.6 + - - -
1097A LEU* 4.0 7.3 - - + +
1098A ASP* 3.0 26.5 + - - +
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Residues in contact with ASP 975 (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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5A MG 2.0 27.1 - - - -
893A ARG* 3.5 43.7 + - + +
894A GLY* 3.6 7.1 - - - -
895A SER 4.0 1.9 + - - -
896A VAL* 4.2 9.0 + - - +
973A ASP* 3.0 14.2 - - - +
974A ILE* 1.3 73.5 - - - +
976A LEU* 1.3 72.6 + - - +
1098A ASP* 3.2 18.1 - - + +
1100A LEU* 4.7 0.8 - - + +
1456A DGT 2.7 31.8 + - - +
17P C 4.1 2.3 - - - +
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Residues in contact with LEU 976 (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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876A SER* 3.9 34.8 - - - +
879A LEU* 5.0 5.2 - - + -
880A VAL* 4.1 18.8 - - + -
890A VAL* 4.3 8.5 - - + -
891A GLY 4.1 3.4 - - - +
892A SER* 5.5 2.7 - - - -
893A ARG* 4.8 1.3 - - - +
907A ILE* 3.4 26.7 - - + +
974A ILE* 4.1 13.2 - - + +
975A ASP* 1.3 81.0 - - - +
977A ASN* 1.3 61.4 + - - +
978A PHE* 3.4 31.3 + - + -
1097A LEU* 5.9 1.3 - - + -
1098A ASP 2.9 10.7 + - - +
1099A ILE* 3.8 4.2 - - + -
1100A LEU* 2.8 32.9 + - - +
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Residues in contact with ASN 977 (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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890A VAL* 3.5 3.1 - - - +
891A GLY* 2.8 46.8 + - - +
892A SER 4.2 3.6 + - - -
893A ARG* 2.6 35.3 + - - +
976A LEU* 1.3 71.3 - - - +
978A PHE* 1.3 64.2 + - - +
1100A LEU* 4.0 5.4 - - - +
1102A HIS* 3.4 30.8 + - + +
1104A ASP* 5.6 0.6 - - - +
1105A PRO* 3.4 6.8 - - + +
1279A TYR* 3.3 33.9 + - - -
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Residues in contact with PHE 978 (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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879A LEU* 3.9 37.2 - - + -
880A VAL 4.5 1.3 - - - -
883A SER* 3.9 5.4 - - - -
890A VAL* 3.7 28.7 - - + +
976A LEU* 3.4 38.4 - - + -
977A ASN* 1.3 75.7 - - - +
979A SER* 1.3 73.4 + - - +
982A TYR* 4.0 18.2 - + + -
983A GLN* 4.4 11.0 - - - +
986A ALA* 3.9 16.2 - - + -
1099A ILE* 3.5 31.6 - - + -
1100A LEU 2.9 15.6 + - - +
1101A GLY* 3.3 0.2 - - - -
1102A HIS* 3.0 21.1 + - - +
1105A PRO* 4.5 2.2 - - - -
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Residues in contact with SER 979 (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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888A TYR* 3.7 29.8 - - - +
889A LEU 4.7 3.0 + - - -
977A ASN 4.1 0.6 + - - -
978A PHE* 1.3 75.9 - - - +
980A GLY* 1.3 58.2 + - - +
981A GLU* 3.1 21.7 + - - +
982A TYR* 2.9 20.3 + - - +
983A GLN* 2.9 13.3 + - - +
1102A HIS 3.8 3.8 - - - -
1105A PRO* 4.2 8.9 - - - +
1106A THR* 2.8 33.4 + - - -
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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