Contacts of the strand formed by residues 125 - 131 (chain C) in PDB entry 3CB4
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 GLU 125 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C GLU 3.0 13.1 + - - +
97C GLY* 3.3 1.9 - - - -
98C ALA 3.1 22.6 + - - +
124C LEU* 1.3 70.4 - - - +
126C VAL* 1.3 68.6 + - - +
127C VAL* 3.3 9.9 + - - +
179C ASP* 3.4 37.6 - - - +
180C ILE* 3.9 16.8 - - + -
181C PRO* 4.0 11.0 - - + -
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Residues in contact with VAL 126 (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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10C ILE* 5.3 2.7 - - + -
98C ALA* 3.3 13.9 - - + +
100C LEU* 3.7 30.7 - - + +
116C CYS* 4.1 15.9 - - - -
119C ALA* 4.1 26.7 - - + +
120C MET* 4.2 15.9 - - + -
124C LEU* 3.2 10.9 + - + +
125C GLU* 1.3 76.0 + - - +
127C VAL* 1.3 62.6 + - - +
128C PRO* 3.5 10.2 - - - +
153C ILE* 4.6 23.8 - - + +
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Residues in contact with VAL 127 (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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98C ALA 2.8 8.5 + - - -
99C LEU* 3.5 21.0 - - + -
100C LEU 2.9 24.6 + - - -
125C GLU* 3.7 21.1 - - - +
126C VAL* 1.3 73.8 - - - +
128C PRO* 1.3 76.8 - - + +
129C VAL* 3.5 8.5 + - + +
159C VAL* 5.3 0.4 - - + -
172C VAL 5.6 1.1 - - - +
175C ARG* 3.8 28.3 - - + -
176C LEU* 4.8 5.6 - - - +
179C ASP* 4.6 11.0 - - + +
180C ILE* 3.9 25.1 - - + -
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Residues in contact with PRO 128 (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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100C LEU* 3.8 10.1 - - + +
126C VAL* 3.5 10.0 - - - +
127C VAL* 1.3 89.8 - - + +
129C VAL* 1.3 63.6 + - - +
147C ILE* 4.9 11.7 - - + -
153C ILE* 4.0 12.6 - - + -
154C ASP 3.5 24.9 - - - +
155C ALA* 4.1 10.5 - - + -
158C ALA* 3.5 32.7 - - + +
159C VAL* 3.5 9.0 + - - +
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Residues in contact with VAL 129 (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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20C LEU* 4.9 2.9 - - + -
99C LEU* 4.4 13.5 - - + -
100C LEU 2.9 11.5 + - - +
101C VAL* 3.5 14.8 - - + -
102C VAL* 3.1 27.2 + - - +
127C VAL* 3.7 19.7 - - + +
128C PRO* 1.3 79.5 - - - +
130C LEU* 1.3 69.1 + - - +
147C ILE* 5.6 1.0 - - - +
159C VAL* 3.3 9.0 - - + +
161C CYS* 3.7 16.2 - - - -
172C VAL* 3.7 42.8 - - + -
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Residues in contact with LEU 130 (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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102C VAL 3.8 4.5 - - - +
104C ALA* 4.5 5.4 - - + -
129C VAL* 1.3 76.3 - - - +
131C ASN* 1.3 60.3 + - - +
133C ILE* 3.9 9.6 - - + +
140C PRO* 4.0 26.2 - - + +
143C VAL* 4.0 27.4 - - + -
144C ALA* 4.8 8.5 - - + +
147C ILE* 4.0 18.6 - - + -
155C ALA 5.6 0.2 - - - +
158C ALA* 4.4 20.2 - - + +
159C VAL 2.8 11.4 + - - +
160C ARG* 3.3 36.3 - - + +
161C CYS* 3.0 28.8 + - - +
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Residues in contact with ASN 131 (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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13C ILE* 6.0 3.2 - - + +
20C LEU* 4.3 9.5 + - - +
23C ARG* 3.1 31.7 + - - +
101C VAL* 3.5 31.0 - - + +
102C VAL 3.0 13.8 + - - +
103C ASP* 4.5 2.0 - - - -
104C ALA* 3.0 25.9 + - - +
129C VAL 3.8 0.2 + - - -
130C LEU* 1.3 71.9 - - - +
132C LYS* 1.3 87.6 + - + +
133C ILE 3.3 3.2 + - - -
161C CYS* 3.4 18.9 + - - -
162C SER 4.0 1.6 + - - -
163C ALA 4.3 0.8 - - - +
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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