Contacts of the strand formed by residues 108 - 119 (chain C) in PDB entry 4OIR
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 ILE 108 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99C GLN* 4.2 24.5 - - + +
100C LEU 3.4 7.0 - - - +
101C ILE* 4.1 25.1 - - + -
106C GLY 3.4 17.2 + - - +
107C LEU* 1.3 83.9 - - - +
109C LYS* 1.3 63.5 + - - +
110C GLU* 4.3 3.0 + - + +
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Residues in contact with LYS 109 (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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99C GLN* 3.3 3.0 - - - -
100C LEU* 2.9 44.6 + - + +
107C LEU* 4.2 9.6 - - + +
108C ILE* 1.3 75.2 - - - +
110C GLU* 1.3 75.5 + - - +
111C ASP* 4.3 17.1 + - - -
367C LEU 4.6 5.2 - - - +
368C THR* 3.7 31.5 - - + +
369C PRO* 3.6 20.4 - - + +
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Residues in contact with GLU 110 (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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69C LEU* 3.8 22.9 - - + +
97C ARG* 3.9 24.8 + - - +
98C LEU 3.5 11.0 - - - +
99C GLN* 3.9 18.7 + - + +
108C ILE* 4.2 4.2 + - + +
109C LYS* 1.3 82.6 + - - +
111C ASP* 1.3 70.2 + - - +
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Residues in contact with ASP 111 (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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96C ALA 3.6 1.2 - - - +
97C ARG* 4.3 4.9 - - - +
98C LEU* 2.9 36.2 + - - +
109C LYS* 4.1 22.1 + - - -
110C GLU* 1.3 79.2 - - - +
112C GLU* 1.3 72.3 + - - +
113C VAL* 3.7 4.5 + - + +
368C THR* 5.3 1.2 - - - -
369C PRO* 4.3 17.0 - - + +
370C ALA* 4.1 20.1 - - - +
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Residues in contact with GLU 112 (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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72C ARG* 2.9 48.6 + - - +
95C TYR* 3.6 28.2 - - + +
96C ALA 3.4 10.3 - - - +
97C ARG* 3.7 34.0 + - - +
111C ASP* 1.3 82.2 + - - +
113C VAL* 1.3 62.3 + - - +
114C PHE 4.2 0.3 + - - -
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Residues in contact with VAL 113 (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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95C TYR* 3.6 4.7 - - - -
96C ALA* 2.9 43.1 + - + +
98C LEU* 3.7 22.0 - - + -
111C ASP* 4.5 4.9 - - - +
112C GLU* 1.3 76.8 - - - +
114C PHE* 1.3 62.1 + - - +
115C LEU* 3.6 20.1 + - + +
369C PRO* 3.7 18.2 - - + +
370C ALA* 3.7 36.6 - - + +
373C VAL* 4.5 5.6 - - + -
280F GLN* 4.7 8.1 - - - +
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Residues in contact with PHE 114 (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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93C PRO* 4.1 11.7 - - + -
94C LEU 4.0 3.6 - - - -
95C TYR* 3.7 30.9 - + + -
112C GLU 4.2 0.6 + - - -
113C VAL* 1.3 72.1 - - - +
115C LEU* 1.3 64.5 + - - +
116C GLY* 3.4 25.4 - - - -
117C HIS* 3.4 24.2 - + - -
373C VAL* 5.8 0.5 - - - +
375C SER* 3.7 11.1 + - - -
279F GLN* 3.5 46.4 + - - -
280F GLN* 3.8 31.9 + - - +
283F GLY* 3.3 33.2 - - - -
284F ARG* 5.0 0.2 - - - -
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Residues in contact with LEU 115 (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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48C PHE* 3.5 35.9 - - + -
52C PHE* 6.5 0.2 - - + -
94C LEU* 2.8 27.6 + - + +
96C ALA* 3.6 20.2 - - + -
98C LEU* 5.8 1.8 - - + -
113C VAL* 3.9 20.6 - - + +
114C PHE* 1.3 77.7 - - - +
116C GLY* 1.3 58.8 + - - +
348C LEU* 5.0 2.7 - - + -
351C LEU* 4.5 11.0 - - + -
373C VAL* 4.0 19.1 - - + -
375C SER* 3.7 15.1 - - - -
378C LEU* 3.6 33.0 - - + +
379C GLU* 3.8 6.2 - - - +
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Residues in contact with GLY 116 (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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94C LEU* 2.8 27.6 + - - +
114C PHE* 3.4 30.3 - - - -
115C LEU* 1.3 80.0 - - - +
117C HIS* 1.3 65.3 + - - -
375C SER* 4.3 0.4 - - - -
379C GLU* 3.7 18.6 - - - -
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Residues in contact with HIS 117 (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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77C PRO* 4.4 18.2 - - + -
91C GLN* 3.2 45.6 + - - +
92C ALA 3.5 4.4 - - - +
93C PRO* 3.7 28.6 - - + +
114C PHE* 3.4 12.4 - + - -
116C GLY* 1.3 80.0 - - - -
118C ILE* 1.3 65.3 + - - +
119C PRO* 4.0 5.8 - - - +
379C GLU* 4.6 11.5 + - - +
382C ILE* 4.2 14.1 - - - +
279F GLN* 6.0 0.2 - - - -
283F GLY 3.2 25.3 + - - -
284F ARG* 4.7 6.0 - - + -
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Residues in contact with ILE 118 (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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26C TYR* 3.6 12.8 - - - +
30C LEU* 4.3 15.9 - - + -
44C ILE* 4.2 19.7 - - + -
73C LEU* 4.4 13.0 - - + -
91C GLN* 3.7 2.5 - - - -
92C ALA* 2.9 34.9 + - - +
94C LEU* 3.8 20.2 - - + -
117C HIS* 1.3 76.6 - - - +
119C PRO* 1.3 81.0 - - + +
120C LEU* 3.5 4.2 + - - +
340C MET* 4.6 7.9 - - - -
344C PHE* 3.5 29.6 - - + -
382C ILE* 4.0 13.2 - - + -
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Residues in contact with PRO 119 (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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26C TYR* 2.7 29.1 + - - -
89C THR* 4.3 8.5 - - + -
90C TYR 3.3 14.4 - - - +
91C GLN* 3.6 6.7 - - + +
117C HIS 4.0 3.1 - - - +
118C ILE* 1.3 91.2 - - + +
120C LEU* 1.3 60.2 + - - +
127C PHE* 4.2 5.6 - - + -
129C ILE* 4.0 20.9 - - + -
382C ILE* 3.8 19.1 - - + -
386C PHE* 3.6 34.5 - - + -
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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