Contacts of the strand formed by residues 1170 - 1177 (chain A) in PDB entry 5IYB
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 THR1170 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1166A LEU* 2.9 25.2 + - - +
1167A ARG* 3.7 10.7 + - - +
1168A LYS 3.6 2.4 - - - +
1169A VAL* 1.3 76.3 - - - +
1171A ALA* 1.3 64.8 + - - +
1172A ASN* 3.3 32.1 - - - +
1173A THR* 4.3 8.3 - - + +
1214A VAL* 3.7 18.9 - - + +
1216A LEU* 3.9 7.4 - - - +
1293A LEU* 3.6 21.0 - - + +
57I LYS* 5.1 7.5 - - + +
59I THR* 4.7 4.0 - - - +
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Residues in contact with ALA1171 (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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1169A VAL 3.4 4.0 + - - -
1170A THR* 1.3 73.4 - - - +
1172A ASN* 1.3 54.5 + - + +
1215A GLU* 2.9 22.2 + - + +
1216A LEU* 3.9 1.3 - - - +
1217A ASP* 3.7 27.8 - - + +
57I LYS* 2.5 29.6 - - - +
58I ILE 4.6 0.3 - - - -
59I THR* 2.8 18.4 + - + +
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Residues in contact with ASN1172 (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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1170A THR* 3.3 14.9 - - - +
1171A ALA* 1.3 81.8 - - + +
1173A THR* 1.3 88.3 + - - +
1174A ALA* 5.2 1.2 - - - +
1213A ARG* 4.9 0.6 - - - +
1214A VAL* 3.4 2.6 - - - -
1215A GLU* 2.6 68.0 + - + +
7I TYR* 3.1 34.3 + - - -
55I VAL* 4.3 0.9 - - - +
56I ASN 3.2 14.8 + - - +
57I LYS* 3.8 7.1 - - - +
58I ILE* 5.3 3.0 - - - +
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Residues in contact with THR1173 (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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1170A THR* 4.3 7.5 - - + +
1172A ASN* 1.3 101.8 + - - +
1174A ALA* 1.3 61.6 - - - +
1212A LEU* 4.5 7.2 - - + -
1213A ARG 3.4 7.0 - - - +
1214A VAL* 4.1 20.6 - - + -
1289A GLU* 3.8 28.8 + - + +
1292A MET* 5.6 3.1 - - + -
1293A LEU* 5.3 5.4 - - + -
54I TYR* 4.9 4.0 - - - -
55I VAL* 3.1 22.8 - - - +
56I ASN* 3.2 26.5 + - - +
57I LYS* 5.6 0.3 - - - +
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Residues in contact with ALA1174 (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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1172A ASN* 5.2 1.1 - - - +
1173A THR* 1.3 77.7 - - - +
1175A ILE* 1.3 62.6 + - - +
1176A TYR* 3.8 33.2 - - + +
1212A LEU* 3.3 5.9 - - - +
1213A ARG* 2.8 43.6 + - + +
7I TYR* 4.0 6.1 - - - +
54I TYR* 3.4 7.6 - - - -
55I VAL* 3.8 11.9 - - + -
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Residues in contact with ILE1175 (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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1174A ALA* 1.3 78.2 - - - +
1176A TYR* 1.3 71.1 + - - +
1210A TRP* 4.1 17.3 - - + -
1211A LEU 3.3 9.9 - - - +
1212A LEU* 4.1 9.6 - - + -
1282A ASP* 4.7 4.9 - - + +
1285A LEU* 3.9 29.2 - - + +
1286A ARG* 4.2 20.6 - - + +
1289A GLU* 6.0 2.9 - - + -
51I SER 3.2 10.2 - - - +
52I CYS* 3.5 0.5 - - - -
53I ILE* 3.4 43.8 + - + +
54I TYR* 3.1 32.9 + - + +
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Residues in contact with TYR1176 (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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1174A ALA* 3.8 21.9 - - + +
1175A ILE* 1.3 87.2 - - - +
1177A TYR* 1.3 59.9 + - - +
1178A ASP 3.5 0.4 + - - -
1185A VAL* 4.3 11.2 - - + -
1186A VAL* 3.7 30.9 - - + +
1210A TRP* 3.7 5.2 - - - -
1211A LEU* 2.7 66.9 + - + +
1213A ARG* 3.8 41.5 + - + -
7I TYR* 4.4 8.0 + - - -
9I PRO* 4.9 9.7 - - + +
50I ASN* 5.1 3.1 - - - -
51I SER* 3.1 5.2 - - - -
52I CYS* 3.5 32.0 - - + -
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Residues in contact with TYR1177 (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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1176A TYR* 1.3 69.7 - - - +
1178A ASP* 1.3 58.9 + - - +
1179A PRO* 3.8 16.1 - - + +
1185A VAL* 3.4 7.8 - - - +
1209A PRO* 3.8 8.3 - - + -
1210A TRP* 4.4 15.5 - + + -
28I GLU* 2.4 47.6 + - + -
29I ASP 3.3 15.6 + - - -
33I ARG* 3.6 28.2 - - + +
34I ILE 3.3 15.8 + - - -
35I LEU* 3.9 40.4 - - + -
51I SER* 2.8 44.2 + - - +
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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