Contacts of the strand formed by residues 102 - 108 (chain C) in PDB entry 2IHU
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 VAL 102 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C GLY 4.7 2.5 - - - +
64C ALA* 3.8 12.8 - - + +
65C ASP* 3.5 25.6 - - + +
75C GLN 3.5 5.8 - - - +
77C CYS* 3.9 28.5 - - - -
91C GLY 6.5 0.4 - - - -
92C ILE* 6.1 2.0 - - + -
95C SER* 3.7 16.6 - - - +
100C SER* 3.0 28.0 + - - +
101C PRO* 1.3 75.6 - - - +
103C ILE* 1.3 72.1 + - - +
104C ALA* 4.2 2.5 - - + +
156C ALA* 4.4 0.2 - - - +
162C GLY 3.6 3.3 + - - +
163C PRO* 3.1 8.1 - - + +
164C SER 2.9 26.5 + - - +
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Residues in contact with ILE 103 (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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22C LEU* 4.2 19.7 - - + -
27C VAL* 5.8 1.6 - - + -
74C PRO* 4.5 11.7 - - + -
75C GLN 2.7 18.8 + - - +
76C ALA* 3.2 9.0 - - + +
77C CYS 3.0 25.5 + - - +
102C VAL* 1.3 78.9 - - - +
104C ALA* 1.3 59.7 + - - +
105C LEU* 3.9 23.9 + - + +
149C VAL* 5.4 2.0 - - + -
152C ALA* 3.9 43.3 - - + +
153C VAL* 3.9 22.0 - - + +
156C ALA* 4.2 7.0 - - + -
164C SER* 3.5 6.5 - - - +
166C ILE* 4.7 4.5 - - + -
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Residues in contact with ALA 104 (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 CYS* 3.8 17.9 - - - -
88C LEU* 4.0 3.8 - - + -
92C ILE* 3.8 36.3 - - + -
102C VAL* 3.7 5.0 + - + +
103C ILE* 1.3 72.2 - - - +
105C LEU* 1.3 61.9 + - - +
163C PRO* 5.2 2.9 - - + -
164C SER 2.9 14.2 + - - +
165C PHE* 3.2 10.6 - - + -
166C ILE 3.0 25.5 + - - -
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Residues in contact with LEU 105 (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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18C LEU* 4.0 15.7 - - + -
22C LEU* 3.9 31.0 - - + -
30C VAL* 5.1 2.9 - - + -
76C ALA* 4.8 4.7 - - + -
77C CYS 3.0 15.3 + - - +
78C TRP* 3.3 37.4 - - + -
79C ALA 3.0 23.0 + - - -
88C LEU* 4.0 3.2 - - - +
103C ILE* 4.0 15.5 - - + +
104C ALA* 1.3 78.4 - - - +
106C ALA* 1.3 61.7 + - - +
165C PHE* 4.4 0.7 - - - -
166C ILE* 3.6 39.5 - - + +
168C LEU* 4.2 6.1 - - + -
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Residues in contact with ALA 106 (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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78C TRP* 5.3 0.4 - - - -
79C ALA* 3.0 14.1 - - + +
80C THR 4.0 2.2 - - - +
85C MET* 3.9 24.2 - - + -
88C LEU* 5.0 2.0 - - + -
105C LEU* 1.3 76.9 - - - +
107C ALA* 1.3 63.8 - - - +
125C SER* 5.9 0.2 - - - -
165C PHE* 3.6 23.9 - - + -
166C ILE 3.2 7.5 + - - +
167C SER* 3.4 4.3 - - - -
168C LEU* 2.8 30.4 + - - +
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Residues in contact with ALA 107 (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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37C GLU* 3.7 45.3 - - + +
78C TRP* 4.9 4.4 - - + -
79C ALA 3.0 8.1 + - - -
80C THR* 4.0 1.0 - - - +
81C LEU* 3.2 28.4 - - + +
85C MET* 5.4 0.2 - - - +
106C ALA* 1.3 79.4 - - - +
108C GLN* 1.3 62.2 + - - +
125C SER* 4.9 4.5 + - - -
167C SER* 4.5 1.4 + - - -
168C LEU* 3.5 10.5 - - + +
170C VAL* 4.0 8.7 - - + -
173C LEU* 5.4 0.4 - - + -
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Residues in contact with GLN 108 (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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81C LEU* 3.8 13.5 - - - +
82C GLY 5.3 0.5 + - - -
107C ALA* 1.3 75.5 - - - +
109C SER* 1.3 94.4 + - - +
114C ILE* 3.9 23.9 - - + +
122C CYS* 3.8 17.0 - - - -
123C LEU 2.9 26.3 + - - +
124C ASP* 4.9 0.8 - - - +
125C SER* 3.6 16.4 + - - +
138C GLU* 4.2 10.2 + - - +
167C SER* 3.4 20.8 + - - +
168C LEU 3.0 4.8 + - - -
169C PRO* 3.8 14.1 - - + -
170C VAL* 3.0 25.8 + - - +
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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