Contacts of the strand formed by residues 76 - 86 (chain C) in PDB entry 2OJW
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 ASP 76 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C ASN* 4.3 19.9 + - + +
62C PHE 3.4 7.9 - - - +
70C SER* 5.3 0.2 - - - -
74C ASN 4.5 0.7 - - - +
75C SER* 1.3 76.3 + - - +
77C MET* 1.3 62.5 + - - +
104C TYR* 4.4 5.5 - - - +
317D ALA* 3.5 18.2 - - - +
319D ARG* 2.8 17.9 + - - +
324D ARG* 2.6 31.8 + - - -
326D PRO* 4.0 1.2 - - - +
327D ARG* 2.8 59.2 + - + +
328D THR 5.1 0.2 + - - -
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Residues in contact with MET 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C ASN* 2.9 27.8 - - - +
62C PHE* 2.8 32.7 + - + +
64C GLY* 3.9 6.7 - - - -
69C GLN* 3.5 33.2 - - + +
70C SER* 3.8 18.8 - - - +
75C SER 3.5 9.0 - - - +
76C ASP* 1.3 79.3 - - - +
78C TYR* 1.3 65.8 + - - +
101C VAL* 3.7 21.1 - - + -
102C PHE 3.8 11.2 - - - +
103C LYS* 3.8 28.0 - - + -
104C TYR 5.1 1.8 - - - +
109C ALA* 4.1 7.6 - - + -
110C GLU* 5.6 0.7 - - - +
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Residues in contact with TYR 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C GLU* 4.2 17.7 - - + -
60C TRP 3.7 9.6 - - - -
61C ASN* 4.4 2.9 - - + +
62C PHE* 4.2 0.2 - - - -
77C MET* 1.3 77.0 - - - +
79C LEU* 1.3 66.0 + - - +
80C VAL* 4.7 4.3 - - + -
100C GLU 3.4 0.4 - - - +
101C VAL* 3.4 10.9 - - - +
102C PHE* 2.9 49.7 + - + +
103C LYS 3.2 28.9 - - - -
104C TYR* 3.8 12.0 + - - -
106C ARG* 3.6 47.5 + - + +
327D ARG* 3.5 27.2 - - + -
328D THR* 5.4 9.6 - - - -
331D GLN* 4.3 9.2 + - + +
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Residues in contact with LEU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 4.2 18.6 - - + -
32C TRP* 3.6 49.6 - - + -
43C LYS* 4.4 4.7 - - - -
59C GLU* 3.6 6.1 - - - +
60C TRP* 3.0 37.6 + - + +
61C ASN 4.0 22.7 - - - +
62C PHE* 3.5 33.7 - - + -
78C TYR* 1.3 73.4 - - - +
80C VAL* 1.3 64.4 + - - +
81C PRO* 3.9 2.2 - - - +
99C CYS* 4.1 15.3 - - + -
100C GLU 3.4 1.8 - - - -
101C VAL* 4.2 2.9 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59C GLU* 4.0 27.4 - - + +
78C TYR* 4.7 6.5 - - + -
79C LEU* 1.3 78.1 - - - +
81C PRO* 1.3 81.1 - - + +
82C ALA* 4.3 0.5 - - - +
99C CYS* 3.3 3.4 - - - +
100C GLU* 2.9 32.3 + - + +
102C PHE* 3.7 35.0 - - + -
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Residues in contact with PRO 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 4.1 6.7 - - + -
54C VAL* 3.6 30.6 - - + +
57C LEU* 3.9 14.8 - - + +
58C PRO 3.7 25.1 - - - +
59C GLU* 4.3 5.6 - - + +
79C LEU 3.9 5.4 - - - +
80C VAL* 1.3 95.4 - - + +
82C ALA* 1.3 60.0 + - - +
97C VAL* 3.7 17.3 - - + -
98C LEU 4.0 5.6 - - - +
99C CYS* 4.0 4.9 - - - -
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Residues in contact with ALA 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 4.0 11.4 - - - +
80C VAL 4.3 4.7 - - - +
81C PRO* 1.3 73.9 - - - +
83C ALA* 1.3 59.8 + - + +
98C LEU* 2.8 21.2 + - + +
99C CYS 4.5 0.4 - - - -
100C GLU* 4.3 9.2 - - + +
114C ARG* 3.6 44.3 + - - +
216C ASP* 4.9 1.3 - - - +
1506C GOL 2.8 18.2 + - - -
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Residues in contact with ALA 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C VAL* 3.9 6.0 - - - +
82C ALA* 1.3 79.3 - - - +
84C MET* 1.3 61.8 + - - +
85C PHE* 3.8 20.8 - - + -
96C LEU 3.8 0.7 - - - +
97C VAL* 3.5 2.9 - - - -
98C LEU* 2.9 39.3 + - + +
216C ASP* 3.8 15.0 - - + +
1506C GOL 3.7 28.5 - - - +
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Residues in contact with MET 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C PRO* 3.9 28.9 - - - +
52C LYS 4.2 3.6 - - - +
53C CYS* 3.8 33.9 - - - +
54C VAL* 3.9 19.0 - - + +
57C LEU* 3.7 25.6 - - + -
83C ALA* 1.3 72.0 - - - +
85C PHE* 1.3 76.1 + - - +
95C LYS* 3.9 27.1 - - + +
96C LEU 3.3 10.1 - - - +
97C VAL* 4.6 0.4 - - - +
1506C GOL 5.1 2.3 + - - -
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Residues in contact with PHE 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ALA* 3.8 25.6 - - + -
84C MET* 1.3 79.4 - - - +
86C ARG* 1.3 67.5 + - - +
95C LYS* 3.5 12.3 - - - +
96C LEU* 2.8 38.5 + - + +
186C ALA* 3.4 20.6 - - + +
187C GLY* 3.8 13.2 - - - -
188C VAL* 3.9 11.4 - - + -
216C ASP 4.7 0.7 - - - -
217C HIS* 3.7 50.7 - + - -
220C VAL* 3.4 39.7 - - + -
1506C GOL 4.3 8.3 - - - -
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Residues in contact with ARG 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B PRO* 5.0 5.5 + - - +
22B GLN 5.8 2.2 + - - -
85C PHE* 1.3 77.6 - - - +
87C ASP* 1.3 59.4 + - - +
88C PRO* 3.3 2.8 - - - +
92C ASP* 3.0 42.9 + - - +
94C ASN 4.0 5.2 - - - -
95C LYS* 4.6 12.1 - - - +
96C LEU* 4.1 2.3 - - - +
184C LEU 4.8 1.6 + - - -
185C TYR* 2.8 72.2 + - + +
186C ALA* 3.0 32.2 + - - +
187C GLY* 5.7 0.9 - - - -
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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