Contacts of the strand formed by residues 137 - 144 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A PHE* 2.8 34.1 + - - +
133A GLN* 3.5 7.4 - - - +
135A GLN 3.4 3.5 + - - +
136A PRO* 1.3 75.6 - - - +
138A VAL* 1.3 63.9 + - - +
139A SER* 2.9 15.6 + - - -
163A PRO* 4.6 11.9 - - + -
164A LEU 3.5 15.5 - - - +
166A TYR* 3.5 10.7 - - - -
1E NAG 1.5 64.8 + - - +
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Residues in contact with VAL 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ILE* 3.9 13.0 - - + -
128A VAL 3.3 12.8 - - - +
129A PHE* 4.1 11.9 - - + -
137A ASN* 1.3 82.6 - - - +
139A SER* 1.3 63.9 + - - +
156A THR* 4.1 3.1 + - - +
164A LEU* 3.3 38.1 + - + +
165A PRO 3.8 21.5 - - - +
166A TYR* 4.5 3.1 - - + -
168A ARG* 5.1 0.4 - - + -
169A ARG* 4.3 19.1 - - + +
648A PHE* 3.7 35.2 - - + -
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Residues in contact with SER 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ALA 3.6 0.9 - - - +
127A ILE* 3.5 2.9 - - - +
128A VAL* 2.9 34.7 + - - +
130A PHE* 3.7 20.8 - - - -
137A ASN* 2.9 22.2 + - - -
138A VAL* 1.3 75.8 + - - +
140A GLU* 1.3 63.0 + - - +
141A LEU* 4.0 16.4 - - - +
154A ASP* 4.1 7.9 + - - -
156A THR* 3.2 10.2 + - - -
1E NAG 3.5 13.9 + - - -
2E NAG 6.0 0.2 - - - -
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Residues in contact with GLU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A LEU* 4.0 13.3 - - + +
126A ALA 3.6 4.5 - - - -
127A ILE* 4.3 18.7 - - + +
138A VAL 4.5 0.2 + - - -
139A SER* 1.3 74.4 - - - +
141A LEU* 1.3 59.0 + - - +
154A ASP* 3.2 7.6 - - - +
155A VAL* 3.2 36.1 + - + -
156A THR* 2.8 11.6 + - - +
159A ARG* 3.3 26.3 + - - -
160A HIS* 2.8 38.1 + - - -
164A LEU* 3.9 4.7 - - + +
648A PHE* 4.3 18.5 - - + -
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A LEU* 4.4 5.4 - - + -
79A LEU* 4.2 11.2 - - + -
124A ALA 3.7 0.5 - - - +
125A LEU* 3.4 5.4 - - - +
126A ALA* 2.8 47.4 + - + +
128A VAL* 3.6 29.2 - - + -
130A PHE* 4.7 3.1 - - + -
139A SER* 4.0 11.4 - - - +
140A GLU* 1.3 82.6 - - - +
142A VAL* 1.3 63.2 + - - +
143A VAL* 3.7 2.5 + - + +
152A MET* 3.9 35.2 - - + -
153A ARG 3.4 5.4 - - - +
154A ASP* 3.8 31.0 - - + +
2E NAG 4.4 10.1 - - + +
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Residues in contact with VAL 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A GLN* 4.5 10.3 - - + +
123A GLU* 3.6 37.5 - - + +
124A ALA 3.4 7.2 - - - +
125A LEU* 4.1 16.2 - - + -
140A GLU 4.5 0.2 + - - -
141A LEU* 1.3 71.8 - - - +
143A VAL* 1.3 63.9 + - - +
151A TYR* 3.9 6.5 - - + +
152A MET* 3.3 4.3 - - - -
153A ARG* 2.9 58.1 + - + +
155A VAL* 3.7 22.7 - - + -
159A ARG* 4.4 8.3 - - - +
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Residues in contact with VAL 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A VAL* 4.1 30.8 - - + +
74A PHE* 3.8 19.5 - - + -
75A LEU* 3.9 27.6 - - + -
123A GLU* 3.5 4.2 - - - +
124A ALA* 2.9 36.3 + - - +
126A ALA* 4.9 2.5 - - + -
141A LEU* 4.3 8.7 - - + +
142A VAL* 1.3 79.7 - - - +
144A GLY* 1.3 60.8 + - - +
146A LEU* 5.3 1.1 - - - +
149A PRO* 3.9 15.0 - - + -
151A TYR* 3.4 14.4 - - - +
152A MET* 4.3 10.1 - - + -
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Residues in contact with GLY 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A ARG 4.2 3.6 - - - -
123A GLU* 4.4 0.9 - - - -
143A VAL* 1.3 79.7 - - - +
145A PRO* 1.4 70.5 - - - +
146A LEU* 5.5 1.3 - - - -
149A PRO* 3.9 1.8 - - - -
150A SER 2.7 25.0 + - - -
151A TYR* 2.7 41.6 + - - -
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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