Contacts of the helix formed by residues 93 - 105 (chain B) in PDB entry 1CP3
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 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92B THR* 1.3 69.9 - - - +
94B GLU* 1.3 74.5 + - - +
96B ILE* 3.6 13.1 + - - +
97B VAL* 3.8 13.0 + - + +
129B GLY* 3.5 6.4 - - - -
131B ASN* 2.7 20.8 + - - +
132B GLY* 3.3 17.9 - - - +
133B PRO* 3.1 30.7 + - - +
134B VAL* 3.7 32.6 - - + +
135B ASP* 5.4 2.4 - - - +
138B LYS* 4.9 15.8 - - - +
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B THR* 2.8 7.8 + - - +
93B ARG* 1.3 95.7 - - - +
95B GLU* 1.3 64.5 + - + +
96B ILE 3.1 2.5 + - - -
97B VAL* 3.5 5.5 + - - +
98B GLU* 3.4 28.5 + - - +
131B ASN* 3.3 28.5 + - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90B ASP 3.9 4.5 - - - +
91B LEU* 3.7 26.8 - - + +
92B THR* 2.8 46.9 + - - +
94B GLU* 1.3 71.4 - - + +
96B ILE* 1.3 64.9 + - - +
98B GLU* 3.7 9.2 - - - +
99B LEU* 3.2 23.4 + - - +
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Residues in contact with ILE 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B ILE* 4.5 19.5 - - + -
52B ASN* 4.3 10.8 - - - +
91B LEU* 3.8 16.2 - - + +
92B THR 3.1 12.6 + - - +
93B ARG 3.8 7.2 - - - +
94B GLU 3.1 0.4 - - - -
95B GLU* 1.3 74.4 - - - +
97B VAL* 1.3 68.2 + - + +
99B LEU* 3.1 16.9 + - - +
100B MET* 3.1 21.2 + - + +
118B LEU* 5.1 6.5 - - + -
127B ILE* 4.4 10.8 - - + -
128B PHE 4.7 0.2 - - - +
129B GLY* 3.9 28.0 - - - -
134B VAL* 4.1 13.5 - - + -
139B ILE* 3.9 29.2 - - + -
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ARG* 3.8 13.9 + - + +
94B GLU* 3.5 7.4 + - - +
96B ILE* 1.3 74.7 - - + +
98B GLU* 1.3 60.6 + - - +
100B MET* 3.9 5.5 - - - -
101B ARG* 2.9 45.6 + - - +
134B VAL* 4.1 20.2 - - + -
138B LYS* 4.2 31.6 - - + +
139B ILE* 5.4 3.8 - - + -
142B PHE* 3.6 28.3 - - + -
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Residues in contact with GLU 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLU 3.4 16.4 + - - +
95B GLU* 3.7 13.5 - - - +
96B ILE 3.1 0.6 - - - -
97B VAL* 1.3 81.3 - - - +
99B LEU* 1.3 57.0 + - - +
101B ARG* 3.1 36.8 + - - +
102B ASP* 2.9 41.9 + - - +
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Residues in contact with LEU 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 4.1 8.7 - - + -
50B ILE* 3.5 32.1 - - + -
86B ARG* 5.4 2.9 - - - +
88B LYS* 3.7 33.4 - - + +
91B LEU* 5.3 4.0 - - + -
95B GLU 3.2 9.7 + - - +
96B ILE* 3.1 9.7 + - + +
98B GLU* 1.3 74.7 - - - +
100B MET* 1.3 68.5 + - + +
101B ARG 3.1 1.3 - - - -
102B ASP* 3.0 8.3 + - + +
103B VAL* 2.7 54.6 + - + +
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Residues in contact with MET 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B ILE* 4.2 23.1 - - + -
50B ILE* 4.8 5.4 - - + -
96B ILE* 3.1 20.5 + - + +
97B VAL* 4.0 2.5 - - - +
99B LEU* 1.3 101.2 - - + +
101B ARG* 1.3 63.2 + - - +
103B VAL* 4.5 4.3 - - + -
104B SER* 3.0 26.9 + - - -
114B PHE* 4.8 2.0 - - + -
116B CYS* 4.2 20.2 - - - -
118B LEU* 6.1 0.4 - - - -
139B ILE* 3.7 28.5 - - + +
142B PHE* 4.0 21.5 - - + +
143B PHE* 3.8 24.3 - - + -
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Residues in contact with ARG 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 2.9 32.5 + - - +
98B GLU* 3.1 37.4 + - - +
100B MET* 1.3 79.4 - - - +
102B ASP* 1.3 63.7 + - - +
104B SER* 3.3 13.9 + - - -
105B LYS* 3.1 38.7 + - + +
142B PHE* 3.5 39.1 - - + -
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Residues in contact with ASP 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B GLU* 2.9 31.2 + - - +
99B LEU* 3.0 9.4 + - + +
101B ARG* 1.3 78.3 - - - +
103B VAL* 1.3 63.1 + - + +
105B LYS* 3.1 39.1 + - - +
106B GLU* 3.4 16.1 + - - +
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Residues in contact with VAL 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B LEU* 4.0 9.2 - - + -
48B ILE* 4.0 13.7 - - + -
86B ARG* 3.7 15.7 - - - +
99B LEU* 2.7 36.6 + - + +
100B MET* 4.0 5.6 - - + +
102B ASP* 1.3 73.0 - - + +
104B SER* 1.3 55.3 + - - +
105B LYS 3.2 1.0 + - - -
106B GLU* 3.3 25.3 + - - +
108B HIS* 2.7 33.5 + - + -
114B PHE* 3.4 36.6 - - + -
143B PHE* 4.0 4.7 - - + -
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Residues in contact with SER 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B MET 3.0 17.0 + - - -
101B ARG* 3.3 9.7 + - - +
103B VAL* 1.3 76.6 - - - +
105B LYS* 1.3 62.1 + - - +
106B GLU 3.4 2.4 + - - +
142B PHE* 3.6 37.5 + - - +
143B PHE* 3.6 20.2 - - - -
147B ARG* 5.8 0.3 - - - +
148B CYS* 3.3 27.0 - - - +
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Residues in contact with LYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B ARG* 3.1 41.8 - - + +
102B ASP* 3.1 32.4 + - - +
103B VAL 3.1 1.2 - - - -
104B SER* 1.3 81.0 - - - +
106B GLU* 1.3 64.5 + - - +
107B ASP 3.9 0.3 + - - -
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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