Contacts of the strand formed by residues 137 - 144 (chain C) in PDB entry 2C10
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 ASN 137 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130C PHE* 2.9 31.4 + - - -
133C GLN* 3.4 9.4 - - - +
135C GLN 3.4 3.8 + - - +
136C PRO* 1.3 74.9 - - - +
138C VAL* 1.3 63.6 + - - +
139C SER* 2.7 16.9 + - - -
156C THR* 6.5 0.2 - - - -
163C PRO* 4.6 11.2 - - + -
164C LEU 3.5 15.7 - - - +
165C PRO* 5.6 0.2 - - + -
166C TYR* 3.3 14.5 - - - -
1K NAG 1.4 62.2 + - - +
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Residues in contact with VAL 138 (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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127C ILE* 3.8 15.9 - - + -
128C VAL 3.3 13.9 - - - +
129C PHE* 4.0 12.3 - - + -
137C ASN* 1.3 82.4 - - - +
139C SER* 1.3 61.9 + - - +
156C THR* 4.0 5.0 - - - +
164C LEU* 3.3 43.9 + - + +
165C PRO 4.1 10.8 - - - +
166C TYR* 4.6 3.6 - - + -
169C ARG* 4.2 20.0 - - + +
648C PHE* 3.7 32.1 - - + -
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Residues in contact with SER 139 (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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126C ALA 3.7 0.7 - - - +
127C ILE* 3.6 3.1 - - - -
128C VAL* 3.0 32.5 + - - +
130C PHE* 3.4 24.2 - - - -
137C ASN* 2.7 24.0 + - - -
138C VAL* 1.3 75.5 + - - +
140C GLU* 1.3 63.4 + - - +
141C LEU* 4.2 8.9 - - - +
154C ASP* 4.0 15.6 + - - -
156C THR* 3.2 11.6 - - - +
1K NAG 3.6 8.5 + - - -
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Residues in contact with GLU 140 (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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125C LEU* 3.9 25.1 - - + +
126C ALA 3.5 3.4 - - - -
127C ILE* 4.5 11.5 - - + +
139C SER* 1.3 75.7 - - - +
141C LEU* 1.3 66.9 + - - +
154C ASP* 3.5 2.1 - - - +
155C VAL* 3.2 30.5 + - + -
156C THR* 2.8 11.6 + - - +
159C ARG* 3.0 29.0 + - - -
160C HIS* 2.8 36.8 + - - -
164C LEU* 4.0 6.0 - - + +
648C PHE* 4.5 17.1 - - + -
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Residues in contact with LEU 141 (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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75C LEU* 4.4 7.0 - - + -
79C LEU* 4.5 11.4 - - + -
124C ALA 3.5 0.7 - - - +
125C LEU* 3.5 7.1 - - - +
126C ALA* 2.8 49.5 + - + +
128C VAL* 3.8 27.1 - - + -
130C PHE* 4.8 4.5 - - + -
139C SER* 4.2 10.3 - - - +
140C GLU* 1.3 84.1 - - - +
142C VAL* 1.3 61.4 + - - +
143C VAL* 3.6 3.1 + - + -
152C MET* 3.9 33.9 - - + -
153C ARG 3.3 5.6 - - - +
154C ASP* 3.8 28.7 - - + +
2K NAG 4.8 10.1 - - + +
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Residues in contact with VAL 142 (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 GLN* 4.5 8.1 - - + +
123C GLU* 3.5 31.9 - - + +
124C ALA 3.5 4.9 - - - +
125C LEU* 4.1 10.1 - - + -
141C LEU* 1.3 71.6 - - - +
143C VAL* 1.3 60.7 + - - +
151C TYR* 3.9 7.6 - - + +
152C MET* 3.3 5.0 - - - -
153C ARG* 2.9 66.9 + - - +
155C VAL* 3.7 29.2 - - + -
159C ARG* 4.3 8.5 - - - +
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Residues in contact with VAL 143 (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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71C VAL* 3.7 32.2 - - + +
74C PHE* 3.8 22.4 - - + -
75C LEU* 3.8 29.6 - - + -
123C GLU* 3.5 3.5 - - - +
124C ALA* 2.9 35.4 + - + +
126C ALA* 4.9 1.3 - - + -
141C LEU* 3.6 7.4 + - + +
142C VAL* 1.3 79.2 - - - +
144C GLY* 1.3 60.8 + - - +
146C LEU* 5.6 1.7 - - + +
149C PRO* 4.0 13.2 - - + -
151C TYR* 3.5 6.7 - - - +
152C MET* 4.2 14.4 - - + -
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Residues in contact with GLY 144 (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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122C ARG 4.2 4.0 - - - -
123C GLU* 4.5 0.9 - - - -
143C VAL* 1.3 79.5 - - - +
145C PRO* 1.4 70.4 - - - +
146C LEU* 5.2 1.8 - - - -
149C PRO* 3.8 1.3 - - - -
150C SER 2.7 23.7 + - - -
151C TYR* 2.8 36.8 + - - -
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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