Contacts of the strand formed by residues 115 - 122 (chain A) in PDB entry 2O5F
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 PHE 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.5 18.2 - - + -
13A ASN 3.2 26.5 - - - -
14A GLU* 3.4 22.7 - - - -
16A ASP* 3.8 33.4 - - + +
32A GLU 3.6 17.0 - - - -
34A VAL 3.1 10.1 + - - +
35A ARG* 3.4 3.2 - - + -
36A VAL* 2.9 24.9 + - - +
78A TYR* 3.9 7.0 - - - +
105A PHE 3.5 5.8 - - - -
106A SER* 3.6 22.4 - - - -
107A PRO* 3.2 29.6 - - + +
108A PHE* 4.0 8.7 - + - -
114A SER* 1.3 76.4 - - - +
116A MET* 1.3 61.2 + - - +
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Residues in contact with MET 116 (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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36A VAL* 3.2 26.7 - - + +
38A ASN* 3.4 27.4 - - - +
78A TYR* 4.0 9.4 + - - -
104A SER* 3.2 6.1 - - - -
105A PHE* 2.9 46.2 + - + +
112A LEU* 3.8 24.0 - - + -
113A SER* 4.4 0.9 - - - +
114A SER 3.5 22.4 - - - +
115A PHE* 1.3 77.6 - - - +
117A CYS* 1.3 62.4 + - - +
118A VAL* 4.2 5.8 - - + -
158A ASP* 4.3 11.0 - - + +
162A LEU* 3.7 23.8 - - + -
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Residues in contact with CYS 117 (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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36A VAL 3.6 4.6 + - - -
37A VAL* 3.6 4.2 - - - -
38A ASN 3.2 22.7 + - - +
78A TYR* 3.7 25.4 - - + -
101A PRO* 4.4 12.1 - - - -
103A ALA 3.5 9.9 - - - -
104A SER* 4.1 11.4 - - - +
116A MET* 1.3 76.8 - - - +
118A VAL* 1.3 66.8 + - - +
119A TYR* 3.4 38.6 - - + +
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Residues in contact with VAL 118 (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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38A ASN* 3.1 17.9 - - + +
40A PHE* 4.3 17.9 - - + -
101A PRO* 3.6 3.1 - - - +
102A LEU* 2.6 32.6 + - + -
103A ALA 2.7 17.7 + - - +
105A PHE* 3.8 32.3 - - + -
116A MET* 4.2 9.0 - - + -
117A CYS* 1.3 77.9 - - - +
119A TYR* 1.3 63.9 + - - +
162A LEU* 3.8 15.3 - - + -
166A CYS* 3.9 22.4 - - - -
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Residues in contact with TYR 119 (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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37A VAL* 4.0 9.4 - - + -
38A ASN 2.9 17.0 + - - -
39A ALA* 3.2 5.0 - - + -
40A PHE* 3.0 24.1 + - - +
78A TYR* 3.2 33.8 - - - +
79A GLU* 3.3 4.8 + - + +
82A PHE* 3.7 52.9 - + + -
99A TRP* 3.6 33.2 - + + -
100A ARG 3.4 4.5 - - - +
101A PRO* 3.7 19.5 - - + -
102A LEU* 4.1 4.4 - - - +
117A CYS* 3.4 32.9 - - + -
118A VAL* 1.3 78.7 - - - +
120A GLU* 1.3 62.8 + - - +
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Residues in contact with GLU 120 (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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40A PHE 3.4 6.7 - - - +
42A ARG* 2.9 44.5 + - + -
98A SER 4.1 0.2 - - - +
99A TRP* 3.1 25.0 - - - -
100A ARG* 2.8 51.9 + - - +
102A LEU* 3.9 17.6 - - + +
119A TYR* 1.3 76.5 - - - +
121A LEU* 1.3 62.2 + - - +
122A ARG* 3.8 13.6 - - - +
167A TYR* 2.7 31.3 + - - +
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Residues in contact with LEU 121 (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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39A ALA* 5.6 1.8 - - + -
40A PHE 2.8 11.1 + - - +
41A LEU* 3.3 26.5 - - + +
42A ARG 2.8 26.7 + - - +
68A VAL* 5.3 6.3 - - + -
82A PHE* 3.8 21.5 - - + -
86A ALA* 5.4 0.9 - - + -
90A LEU* 5.2 8.3 - - + -
92A VAL* 3.8 29.6 - - + -
94A ILE* 4.0 20.4 - - + -
97A LEU* 4.1 11.7 - - + -
98A SER 3.7 4.3 - - - +
99A TRP* 3.5 24.0 - - + -
119A TYR 4.2 0.4 - - - -
120A GLU* 1.3 73.6 - - - +
122A ARG* 1.3 64.4 - - - +
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Residues in contact with ARG 122 (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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41A LEU* 4.4 0.2 - - - -
42A ARG* 3.0 37.1 + - - +
43A ASN 3.1 29.7 + - - -
44A SER* 4.0 7.9 - - - +
97A LEU* 4.1 14.4 - - - +
98A SER* 2.8 43.2 + - - +
99A TRP* 5.4 0.9 - - - -
100A ARG* 5.0 7.4 - - - +
120A GLU* 3.8 26.7 - - - +
121A LEU* 1.3 79.5 - - - +
123A SER* 1.3 65.9 + - - +
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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