Contacts of the strand formed by residues 1070 - 1076 (chain A) in PDB entry 5FWW
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 TYR1070 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1065A ASN* 2.7 39.4 + - + +
1068A LYS* 3.8 23.3 - - + -
1069A GLY* 1.3 84.9 - - - +
1071A MET* 1.3 55.5 + - - +
1072A TYR* 4.1 19.7 - - + +
1085A ARG* 3.7 39.0 - - + -
1086A ALA 3.3 20.2 - - - +
1087A ALA* 4.0 7.4 - - + +
1088A LEU* 3.9 7.6 - - - +
1092A GLU* 3.3 32.4 + - + -
1094A GLU* 5.1 2.9 - - - -
1220A VAL 5.5 2.2 - - - -
1221A LYS 6.5 0.4 - - - -
1222A GLY* 6.4 1.6 - - - -
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Residues in contact with MET1071 (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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1029A TYR* 4.2 20.6 - - - -
1038A ILE* 3.9 31.0 - - + -
1051A VAL* 4.0 18.6 - - + -
1052A LEU* 4.7 3.4 - - + -
1062A ILE* 4.3 9.2 - - + -
1063A VAL 3.7 9.6 - - - +
1064A VAL* 4.1 7.4 - - + +
1070A TYR* 1.3 73.7 - - - +
1072A TYR* 1.3 64.7 + - - +
1073A PHE* 4.3 5.0 - - + -
1084A GLU 4.1 0.5 - - - +
1085A ARG* 3.6 4.3 - - - +
1086A ALA* 2.7 51.8 + - + +
1087A ALA 3.6 18.6 - - - +
1088A LEU* 3.8 19.7 - - + -
1090A GLY* 4.5 6.5 - - - +
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Residues in contact with TYR1072 (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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1062A ILE* 3.6 1.5 - - - +
1063A VAL* 2.8 48.1 + - + +
1065A ASN* 4.2 10.4 + - + -
1070A TYR* 4.1 20.1 - - + +
1071A MET* 1.3 77.8 - - - +
1073A PHE* 1.3 64.1 + - - +
1083A ILE* 5.5 1.6 - - + -
1084A GLU 3.6 4.0 - - - +
1085A ARG* 3.4 31.2 + - + -
1096A LEU* 3.8 14.4 - - + -
1107A LEU* 3.4 7.9 - - + +
1109A LEU* 3.6 25.4 - - + -
1116A LEU* 3.6 31.9 - - + -
1131A LEU* 3.1 52.4 + - + +
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Residues in contact with PHE1073 (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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1038A ILE* 3.9 17.5 - - + -
1052A LEU* 3.4 38.6 - - + -
1059A PRO* 4.2 11.4 - - + -
1061A ALA 3.2 15.9 - - - +
1062A ILE* 4.1 12.3 - - + -
1071A MET* 4.3 10.5 - - + -
1072A TYR* 1.3 76.3 - - - +
1074A THR* 1.3 67.8 - - - +
1075A ASN* 4.1 13.9 - - + -
1083A ILE* 3.7 1.7 - - - +
1084A GLU* 3.0 71.9 + - + -
1086A ALA* 4.2 16.8 - - + -
1093A ARG* 4.4 2.2 - - + -
1107A LEU* 3.5 8.8 - - - +
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Residues in contact with THR1074 (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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1059A PRO* 3.7 1.2 - - - +
1060A ARG* 3.1 26.2 + - - +
1061A ALA* 2.9 32.8 + - + +
1073A PHE* 1.3 71.7 - - - +
1075A ASN* 1.3 60.8 + - - +
1076A LEU* 3.6 5.8 + - - +
1082A LYS 3.8 4.7 - - - -
1083A ILE* 4.4 4.7 - - + +
1104A PRO* 3.4 47.1 + - + +
1105A ILE 4.7 0.4 - - - +
1107A LEU* 3.6 32.3 - - + -
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Residues in contact with ASN1075 (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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1057A ASP* 3.6 19.2 + - - -
1058A ARG 2.7 36.5 + - - +
1059A PRO* 3.9 2.0 - - - -
1073A PHE* 3.7 12.6 + - + -
1074A THR* 1.3 68.7 - - - +
1076A LEU* 1.3 58.4 + - - +
1077A GLN* 3.0 30.4 + - - +
1082A LYS* 2.8 36.1 + - + +
1084A GLU* 2.8 36.1 + - - +
1093A ARG* 4.0 4.6 - - - +
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Residues in contact with LEU1076 (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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1017A TYR* 5.2 5.2 - - - +
1058A ARG* 3.0 37.4 + - + +
1060A ARG* 3.8 34.1 - - + +
1074A THR* 4.2 4.3 - - - +
1075A ASN* 1.3 70.6 - - - +
1077A GLN* 1.3 64.8 + - - +
1081A PRO* 4.2 10.8 - - + -
1082A LYS 5.2 0.2 - - - +
1102A SER 5.4 0.2 - - - +
1103A LYS* 5.1 8.7 - - + -
1104A PRO* 3.7 50.9 - - + +
1105A ILE* 5.7 4.9 - - + -
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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