Contacts of the strand formed by residues 111 - 121 (chain A) in PDB entry 2OKD
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 ARG 111 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A GLN* 5.7 3.4 + - - -
33A ASP* 3.6 38.9 + - + +
34A LEU 3.4 8.3 - - - +
35A TYR* 3.8 13.8 - - + -
69A ARG* 3.4 51.1 - - - +
71A GLY* 6.1 1.6 - - - +
72A LEU* 4.1 13.6 - - - +
109A GLY 3.7 2.8 + - - -
110A ASP* 1.3 73.8 - - - +
112A ILE* 1.3 63.1 + - - +
113A ALA 4.3 2.7 - - - +
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Residues in contact with ILE 112 (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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34A LEU* 2.8 19.3 + - + +
36A SER* 3.7 13.2 - - - +
50A ILE* 3.7 22.9 - - + -
52A THR* 3.9 12.8 - - + -
69A ARG* 5.0 4.4 + - - -
72A LEU* 3.8 22.1 - - + +
79A ILE* 4.2 3.1 - - - +
94A VAL* 3.7 31.2 - - + -
96A LEU* 3.9 28.6 - - + +
104A PHE* 6.3 0.4 - - + -
106A VAL* 3.9 26.5 - - + -
110A ASP* 3.5 15.0 - - + +
111A ARG* 1.3 75.0 - - - +
113A ALA* 1.3 66.0 + - - +
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Residues in contact with ALA 113 (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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33A ASP* 3.4 6.4 - - - +
34A LEU* 2.7 37.0 + - + +
66A ILE* 3.7 26.7 - - + -
67A ALA 3.5 14.4 - - - +
69A ARG* 4.5 12.9 - - - +
79A ILE* 4.2 4.7 - - + -
94A VAL* 4.2 7.2 - - + -
111A ARG* 3.8 3.2 - - - +
112A ILE* 1.3 85.6 - - + +
114A GLN* 1.3 58.1 + - - +
115A LEU 4.2 0.2 - - - -
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Residues in contact with GLN 114 (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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29A ALA* 5.8 0.2 - - - +
30A ALA* 3.9 10.7 + - - +
31A GLY 4.5 2.6 + - - -
32A TYR 3.1 16.4 - - - +
33A ASP* 4.4 2.9 - - - +
34A LEU* 4.8 1.1 - - - -
65A ARG 3.3 1.6 - - - +
67A ALA* 2.8 46.6 + - + +
68A PRO 3.1 21.2 + - - +
69A ARG* 3.7 35.0 + - - +
70A SER* 5.3 2.2 + - - +
113A ALA* 1.3 76.6 - - - +
115A LEU* 1.3 62.5 + - - +
116A ILE* 4.6 3.6 - - + -
83B VAL* 3.6 26.6 + - - +
85B ASP* 3.7 19.9 + - - +
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Residues in contact with LEU 115 (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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22A PRO* 6.0 1.6 - - + -
31A GLY* 3.2 6.1 - - - -
32A TYR* 2.6 45.4 + - + +
34A LEU* 4.1 26.3 - - + +
56A MET* 3.6 21.1 - - + -
58A MET* 5.1 1.3 - - + -
64A GLY* 3.7 31.4 - - - -
65A ARG 3.3 7.9 - - - +
66A ILE* 3.9 17.7 - - + -
84A ILE* 4.2 6.7 - - + -
92A ILE* 5.0 3.8 - - + -
113A ALA 4.2 0.4 - - - -
114A GLN* 1.3 71.0 - - - +
116A ILE* 1.3 59.3 + - - +
117A TYR* 3.6 34.1 + - + +
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Residues in contact with ILE 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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30A ALA* 3.5 25.8 - - + +
63A TYR 3.3 0.5 - - - +
64A GLY* 3.4 1.5 - - - -
65A ARG* 2.8 38.6 + - + +
67A ALA* 3.4 30.7 - - + -
114A GLN* 4.0 6.5 - - + +
115A LEU* 1.3 77.1 - - - +
117A TYR* 1.3 60.5 + - - +
118A GLN* 3.2 16.5 + - + +
63B TYR* 3.8 21.8 - - + +
83B VAL* 3.8 25.6 - - + -
120B ILE* 3.5 31.9 - - + -
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Residues in contact with TYR 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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10A VAL* 3.9 4.4 - - + +
30A ALA 4.9 1.2 + - - -
31A GLY* 5.6 1.3 - - - -
32A TYR* 3.7 29.6 - + - -
56A MET* 3.2 31.5 - - - +
58A MET* 3.5 35.0 - - + -
59A PRO* 3.9 23.6 - - + -
62A CYS* 4.5 8.3 - - + -
63A TYR 3.6 3.6 - - - -
64A GLY* 4.8 1.1 - - - -
115A LEU* 3.6 18.3 - - + +
116A ILE* 1.3 69.2 - - - +
118A GLN* 1.3 60.8 + - - +
119A ARG 3.8 0.3 + - - -
120B ILE* 3.3 7.3 - - - +
121B TYR* 3.1 45.8 + - + +
123B PRO* 3.5 27.8 - - + -
125B LEU* 3.7 9.5 - - + +
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Residues in contact with GLN 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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62A CYS* 3.2 5.7 - - - -
63A TYR* 2.8 57.1 + - + +
65A ARG* 3.4 16.4 + - + +
116A ILE* 3.4 24.6 - - + +
117A TYR* 1.3 72.1 - - - +
119A ARG* 1.3 64.8 + - - +
120A ILE* 3.3 4.2 + - - +
200A CL 3.2 3.0 - - - +
204A EDO 2.8 27.3 + - - +
63B TYR* 2.6 33.0 + - - -
118B GLN* 3.9 3.8 - - - -
119B ARG 4.1 2.7 - - - -
120B ILE* 4.3 1.8 - - + -
118C GLN* 2.9 18.8 - - - +
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Residues in contact with ARG 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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60A LYS 5.9 1.0 + - - -
61A PHE 3.6 9.1 + - - +
62A CYS* 4.4 5.4 - - - -
118A GLN* 1.3 69.3 - - - +
120A ILE* 1.3 60.2 + - - +
204A EDO 2.8 23.0 - - - -
119B ARG* 3.1 55.5 + - + +
120B ILE 3.6 23.7 + - - -
121B TYR* 4.3 25.6 - - + +
119C ARG* 3.1 42.6 + - - +
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Residues in contact with ILE 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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61A PHE* 3.0 39.1 + - - +
62A CYS* 3.8 15.3 - - - +
63A TYR* 3.6 8.7 - - + +
118A GLN 3.6 5.4 - - - +
119A ARG* 1.3 81.4 - - - +
121A TYR* 1.3 62.7 + - - +
122A TYR* 3.5 26.0 - - + +
204A EDO 3.5 15.3 - - - +
30C ALA* 3.4 31.4 - - - +
116C ILE* 3.4 22.0 - - + -
117C TYR 3.4 11.9 - - - +
118C GLN* 4.1 0.4 - - - -
119C ARG* 3.6 14.9 + - - -
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Residues in contact with TYR 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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61A PHE* 5.5 1.1 - - - -
120A ILE* 1.3 79.7 - - - +
122A TYR* 1.3 76.8 + - - +
123A PRO* 3.3 45.9 - - + +
7C ASN* 3.6 42.1 + - + -
8C SER 3.1 24.9 + - - -
10C VAL* 4.6 0.6 - - + +
30C ALA 5.1 1.6 - - - +
32C TYR* 4.6 0.7 - - - -
59C PRO* 3.7 34.9 - - + +
62C CYS* 4.3 7.4 - - - -
117C TYR* 3.1 25.7 + - + +
119C ARG* 4.2 14.4 - - + -
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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