Contacts of the strand formed by residues 156 - 163 (chain C) in PDB entry 2X2D
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 ILE 156 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10C ILE* 4.1 11.7 - - + -
11C ALA 3.4 5.4 - - - +
12C VAL* 4.7 10.3 - - + +
52C CYS* 3.2 6.5 - - - +
53C PHE* 3.0 35.0 + - + +
56C ILE* 2.9 36.6 - - + -
142C MET* 3.6 39.7 - - + +
145C PHE* 4.0 20.6 - - + -
152C THR* 3.6 19.2 + - + -
154C LYS 3.2 10.9 + - - +
155C LYS* 1.3 71.8 - - - +
157C THR* 1.3 59.7 + - - +
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Residues in contact with THR 157 (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* 3.6 9.1 - - - +
11C ALA* 2.9 46.4 + - - +
14C GLY* 5.2 5.0 + - - +
50C GLY* 4.5 8.5 - - - +
51C SER 3.2 10.1 - - - +
52C CYS* 4.5 3.6 - - + -
53C PHE* 5.1 0.2 - - - -
155C LYS* 3.6 50.6 + - + +
156C ILE* 1.3 76.8 - - - +
158C ILE* 1.3 65.9 + - - +
159C ALA* 3.4 5.8 + - - +
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Residues in contact with ILE 158 (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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8C PHE* 3.6 37.5 - - + -
9C ASP 3.8 2.7 - - - -
10C ILE* 4.0 5.4 - - + -
48C TYR* 3.7 17.0 - - + +
49C LYS 3.8 0.3 - - - -
50C GLY* 2.7 30.3 + - - -
51C SER* 2.7 27.4 + - - +
52C CYS 5.6 0.9 - - - +
53C PHE* 3.6 27.4 - - + -
65C GLY 5.5 2.5 - - - +
112C PHE* 4.3 7.9 - - + -
157C THR* 1.3 71.8 - - - +
159C ALA* 1.3 62.4 + - - +
160C ASP 3.2 20.9 + - - +
161C CYS* 3.7 23.3 - - + -
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Residues in contact with ALA 159 (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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9C ASP* 2.9 20.0 + - + +
10C ILE 5.1 0.2 - - - -
11C ALA* 4.1 21.8 - - + -
49C LYS* 3.9 15.8 - - - +
50C GLY* 4.8 2.2 + - - +
157C THR* 3.4 7.0 + - - +
158C ILE* 1.3 73.5 - - - +
160C ASP* 1.3 62.8 + - + +
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Residues in contact with ASP 160 (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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7C PHE* 4.2 9.8 - - + -
9C ASP* 2.9 45.0 + - + +
49C LYS* 3.4 28.5 + - - +
158C ILE* 3.1 7.2 - - - +
159C ALA* 1.3 84.6 - - + +
161C CYS* 1.3 91.4 + - - +
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Residues in contact with CYS 161 (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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7C PHE* 3.1 28.3 - - - +
8C PHE* 3.7 13.0 - - + -
40C SER* 3.2 26.8 - - - +
41C THR* 4.7 3.3 - - - +
48C TYR* 4.0 11.2 - - - -
49C LYS* 3.7 34.1 - - - +
158C ILE* 3.7 10.3 - - - -
160C ASP* 1.3 92.8 + - - +
162C GLY* 1.3 60.5 + - - +
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Residues in contact with GLY 162 (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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6C VAL* 3.3 11.1 - - - +
7C PHE* 2.8 44.3 + - - -
40C SER 3.3 14.1 + - - -
41C THR* 4.2 7.0 - - - -
161C CYS* 1.3 78.1 - - - +
163C GLN* 1.3 58.1 + - - -
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Residues in contact with GLN 163 (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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4C PRO* 4.2 7.9 - - - +
5C THR 3.3 16.2 - - - +
6C VAL* 4.3 2.7 - - + +
7C PHE* 4.1 4.5 - - - -
37C ARG* 3.2 45.7 + - + +
41C THR* 3.8 15.8 - - + +
162C GLY* 1.3 71.2 - - - -
164C LEU* 1.3 61.5 + - - +
165C GLU* 3.3 29.9 + - - +
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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