Contacts of the strand formed by residues 85 - 93 (chain F) in PDB entry 6ULG
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 85 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9F LYS* 3.8 6.5 - - + +
11F LEU* 3.7 28.5 - - + -
81F ILE 4.2 1.8 - - - +
82F PHE* 3.4 42.8 - - + +
84F ASN* 1.3 75.4 - - - +
86F GLU* 1.3 63.6 + - - +
87F VAL 3.6 24.0 - - - +
88F LEU* 4.4 1.3 - - + +
113F ILE* 3.9 26.9 - - + -
117F SER* 3.6 14.3 + - - +
119F ASP 5.3 1.0 - - - +
120F ALA* 3.9 10.7 - - - +
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Residues in contact with GLU 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F LYS* 3.6 39.6 - - + +
9F LYS 2.8 18.7 + - - +
58F LEU* 3.9 21.7 - - + +
84F ASN 3.8 1.2 + - - -
85F VAL* 1.3 74.6 - - - +
87F VAL* 1.3 71.2 + - + +
119F ASP 4.7 5.2 - - - +
120F ALA* 3.3 8.9 - - - +
121F LYS* 3.1 30.0 + - - +
180F LEU* 4.6 12.2 - - + +
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Residues in contact with VAL 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F LYS 3.6 2.4 + - - -
10F VAL* 3.3 16.9 - - + +
11F LEU 2.9 26.3 + - - -
85F VAL* 3.6 7.9 - - - +
86F GLU* 1.3 91.2 - - + +
88F LEU* 1.3 60.5 + - - +
89F ILE* 3.7 27.4 - - + -
120F ALA* 4.9 0.4 - - - -
121F LYS* 3.3 23.1 - - + +
123F PHE* 3.7 12.6 - - + -
176F ILE* 5.0 0.7 - - + -
180F LEU* 3.6 36.8 - - + -
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Residues in contact with LEU 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.1 7.9 - - + +
13F MET* 3.7 26.2 - - + -
82F PHE* 4.1 10.1 - - + -
85F VAL* 4.4 2.4 - - + +
87F VAL* 1.3 72.2 - - - +
89F ILE* 1.3 58.5 + - - +
90F TYR* 3.7 37.5 - - + +
106F TYR* 4.6 1.6 - - + -
109F CYS* 4.4 10.1 - - + +
113F ILE* 3.7 38.6 - - + +
121F LYS 3.3 5.7 + - - +
122F ILE* 3.4 24.8 - - + -
123F PHE* 2.7 34.7 + - - +
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Residues in contact with ILE 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.9 17.3 - - + -
11F LEU 3.0 13.0 + - - +
12F LEU* 3.4 22.2 - - + +
13F MET 3.1 23.2 + - - -
60F LEU* 5.3 0.2 - - + -
87F VAL* 3.7 19.3 - - + -
88F LEU* 1.3 71.0 - - - +
90F TYR* 1.3 61.1 + - - +
91F VAL* 4.4 4.0 - - + -
123F PHE* 3.6 7.0 - - + +
125F LEU* 3.7 31.4 - - + -
173F TRP* 3.7 32.1 - - + -
176F ILE* 4.0 22.9 - - + -
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Residues in contact with TYR 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F MET* 3.2 27.8 - - + -
14F GLY 3.7 16.7 + - - -
64F GLY 6.1 0.7 - - - -
65F GLY* 5.5 1.4 - - - -
88F LEU* 3.7 16.3 - - + -
89F ILE* 1.3 72.5 - - - +
91F VAL* 1.3 67.7 + - - +
92F PHE* 3.5 35.0 + + + -
102F ASP* 4.3 6.6 + - + -
105F TYR* 3.6 27.4 - - - +
106F TYR* 3.5 44.9 - + + -
109F CYS* 4.0 25.0 - - + -
123F PHE 2.9 10.2 + - - +
124F CYS* 3.3 5.3 - - - +
125F LEU* 2.9 25.1 + - - +
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Residues in contact with VAL 91 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 3.7 28.0 - - + -
13F MET 3.2 10.4 + - - +
14F GLY* 3.3 27.0 - - - -
15F LYS 4.0 0.2 + - - -
18F SER* 3.5 25.2 + - - +
20F LYS* 4.8 4.0 - - + +
23F MET* 3.9 22.7 - - + -
89F ILE* 4.4 2.2 - - + -
90F TYR* 1.3 78.0 - - - +
92F PHE* 1.3 66.2 + - - +
125F LEU* 3.6 15.7 - - + +
127F HIS* 3.7 24.5 - - + -
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Residues in contact with PHE 92 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 5.7 4.0 - - + -
18F SER* 4.3 4.9 - - - -
90F TYR* 3.5 33.9 - + + -
91F VAL* 1.3 74.6 - - - +
93F ASP* 1.3 65.7 + - - +
99F LEU* 5.1 11.2 - - + -
102F ASP* 4.6 25.8 - - + +
103F MET* 5.4 4.9 - - + -
106F TYR* 4.8 8.1 - + + -
124F CYS* 4.6 11.2 - - + -
125F LEU 3.2 7.7 + - - +
126F VAL* 3.4 12.9 - - + +
127F HIS* 3.0 21.2 + - - -
144F ARG* 4.1 27.4 - - + -
148F LEU* 3.6 42.0 - - + -
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Residues in contact with ASP 93 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F LYS* 4.1 10.2 - - - +
17F GLY 4.9 0.3 - - - +
18F SER* 3.4 26.1 + - - -
92F PHE* 1.3 82.1 - - - +
94F VAL* 1.3 63.1 + - - +
95F GLU* 4.1 14.1 - - - +
96F SER* 3.4 30.7 + - - -
99F LEU* 5.8 0.9 - - - +
126F VAL* 5.1 0.4 - - - -
127F HIS* 3.3 16.8 - - + +
128F LYS* 3.5 33.6 + - + +
144F ARG* 3.9 8.2 + - - -
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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