Contacts of the strand formed by residues 108 - 114 (chain W) in PDB entry 5A0Q
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 PRO 108 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7W VAL* 4.3 17.5 - - + -
8W TYR 4.8 1.1 - - - +
9W LYS 4.9 5.4 - - - +
10W ASP 4.8 3.8 - - - +
11W GLY* 3.8 22.4 - - - +
12W ILE* 3.5 19.3 - - + -
102W GLY 3.6 8.1 - - - +
103W VAL* 3.7 10.3 - - + -
107W GLY* 1.3 85.6 - - - +
109W HIS* 1.3 71.9 + - - +
121W LYS* 3.6 11.1 - - - -
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Residues in contact with HIS 109 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7W VAL* 4.7 0.4 - - - -
12W ILE* 3.5 3.8 - - - +
76W VAL* 3.3 30.3 - - + +
77W VAL* 4.0 17.8 - - + +
101W GLY* 3.4 2.3 - - - -
102W GLY 3.0 30.4 + - - +
106W THR* 3.3 35.8 + - - -
107W GLY 3.3 8.7 + - - -
108W PRO* 1.3 85.8 + - - +
110W LEU* 1.3 60.9 + - - +
111W TYR* 3.5 28.7 - + + -
121W LYS* 3.8 22.9 - - + +
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Residues in contact with LEU 110 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5W GLY* 3.5 30.5 - - - +
6W VAL* 3.6 15.9 - - - +
7W VAL* 3.4 15.4 - - + +
12W ILE* 3.8 7.6 - - + -
14W LEU* 3.7 19.5 - - + -
99W VAL* 3.4 32.8 - - + -
100W LEU 3.3 10.5 - - - +
101W GLY* 4.2 0.2 - - - -
109W HIS* 1.3 75.5 - - - +
111W TYR* 1.3 59.2 + - - +
112W SER 4.0 0.3 + - - -
120W ASP 4.0 0.3 - - - +
121W LYS* 3.2 22.1 - - - +
122W LEU 3.3 23.7 + - - +
123W PRO 3.9 1.1 - - - +
125W VAL* 4.1 11.7 - - + +
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Residues in contact with TYR 111 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76W VAL* 4.8 0.2 - - + -
77W VAL* 3.6 23.2 - - + +
80W ASN* 2.5 49.6 - - + +
99W VAL* 4.6 2.7 - - - -
100W LEU 2.9 31.3 + - - -
109W HIS* 3.5 25.5 - + + -
110W LEU* 1.3 77.5 - - - +
112W SER* 1.4 67.0 + - - +
113W ILE* 3.4 7.8 - - + +
119W THR* 3.7 20.9 - - - -
120W ASP* 3.5 8.5 - - - +
121W LYS* 3.1 34.7 - - + +
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Residues in contact with SER 112 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98W LEU 3.9 4.0 - - - -
99W VAL* 4.5 1.6 - - - +
110W LEU 4.0 1.8 + - - -
111W TYR* 1.4 71.5 - - - +
113W ILE* 1.3 59.0 + - - +
114W TYR* 3.6 29.2 + - - -
118W SER 3.5 1.4 - - - +
119W THR* 3.5 2.3 - - - -
120W ASP* 3.1 32.9 + - - +
125W VAL* 3.8 35.0 - - - +
126W THR 4.2 5.8 + - - -
127W MET* 3.3 18.9 - - - +
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Residues in contact with ILE 113 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80W ASN* 3.6 16.8 - - - +
83W LEU* 3.5 43.5 - - + +
84W LYS* 4.9 0.2 - - - -
87W LEU* 3.5 22.5 - - + +
97W ALA* 3.4 4.3 - - - +
98W LEU* 2.9 38.8 + - + +
100W LEU* 4.3 4.7 - - + -
111W TYR 3.4 13.9 - - - +
112W SER* 1.3 79.9 + - - +
114W TYR* 1.3 65.2 + - - +
117W GLY* 4.7 2.2 - - - -
118W SER 3.0 17.7 - - - +
119W THR* 3.5 19.3 - - + -
127W MET* 3.5 1.9 - - - +
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Residues in contact with TYR 114 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22V THR* 5.6 4.9 - - + -
25V TYR* 5.5 3.1 - - - -
27V ALA* 3.7 28.6 - - + +
300V KNM 4.0 36.8 - - + -
87W LEU* 3.9 2.1 - - - +
97W ALA* 4.2 1.1 - - + -
112W SER* 3.6 30.2 + - - -
113W ILE* 1.3 78.8 - - - +
115W PRO* 1.3 71.1 - - + +
116W HIS 3.1 3.8 - - - +
117W GLY* 2.9 21.5 + - - -
118W SER* 3.2 23.0 + - - -
120W ASP* 5.1 10.5 - - + -
126W THR 4.5 7.6 + - - -
127W MET* 4.6 16.4 - - + -
135W MET* 5.0 8.3 - - - +
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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