Contacts of the strand formed by residues 156 - 163 (chain H) in PDB entry 2A2Q
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 MET 156 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16H ILE* 3.7 20.6 - - + +
19H GLY 5.6 1.3 - - - -
20H LYS* 3.3 11.7 - - - +
21H VAL* 3.6 36.3 - - + -
22H CYS* 4.5 0.4 - - - -
139H SER* 3.0 8.4 - - - -
140H GLY 2.9 36.8 + - - +
144H LEU* 3.8 30.7 - - + -
152H ALA* 3.7 19.1 - - + -
153H LEU 5.3 0.2 - - - +
154H GLU* 3.2 23.8 - - + +
155H LEU* 1.3 74.8 - - - +
157H VAL* 1.3 62.2 + - - +
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Residues in contact with VAL 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 4.4 1.8 - - - -
19H GLY* 3.4 2.4 - - - -
20H LYS* 2.8 39.5 + - + +
21H VAL 4.2 2.9 - - - +
22H CYS* 3.6 34.3 - - + -
23H PRO* 5.1 2.0 - - + -
27H CYS* 4.1 9.2 - - - -
137H LEU* 3.9 35.0 - - + -
138H VAL 3.3 11.4 - - - +
139H SER* 4.1 7.2 - - - -
156H MET* 1.3 76.2 - - - +
158H LEU* 1.3 64.3 + - - +
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16H ILE* 3.7 11.4 - - + -
17H VAL 4.0 3.1 - - - +
18H GLY 3.7 22.7 - - - +
19H GLY* 3.8 5.6 - - - -
137H LEU* 3.2 9.2 - - - -
138H VAL* 2.9 39.5 + - + +
157H VAL* 1.3 76.8 - - - +
159H ASN* 1.3 67.6 + - - +
160H VAL* 3.5 24.2 - - + -
188H LYS* 3.7 26.2 - - + +
189H ASP* 3.3 40.8 - - - +
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Residues in contact with ASN 159 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PHE* 3.2 39.4 - - + +
136H SER* 3.1 16.1 + - - +
137H LEU* 3.4 19.2 - - + +
158H LEU* 1.3 79.4 - - - +
160H VAL* 1.3 60.8 + - - +
184H TYR* 2.8 26.2 + - - -
188H LYS* 5.0 0.7 + - - +
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Residues in contact with VAL 160 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H ARG 3.7 0.3 - - - +
135H PHE* 3.4 4.5 - - - -
136H SER* 2.8 40.4 + - - +
138H VAL* 3.8 29.4 - - + -
158H LEU* 3.5 32.5 - - + -
159H ASN* 1.3 75.8 + - - +
161H PRO* 1.3 67.6 - - + +
162H ARG 4.0 0.2 + - - -
183H ALA* 3.9 17.7 - - + -
184H GLY* 3.8 25.1 - - + +
189H ASP* 5.2 2.5 - - - +
199H HIS* 4.1 6.5 + - + -
228H TYR* 4.6 5.8 - - - +
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Residues in contact with PRO 161 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H ARG* 3.2 22.2 - - - +
135H PHE* 3.8 19.7 - - + -
160H VAL* 1.3 86.9 - - + +
162H ARG* 1.3 62.1 - - - +
163H LEU* 3.7 7.7 - - + +
183H ALA* 3.1 3.7 - - - -
184H GLY* 2.9 74.6 + - + +
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Residues in contact with ARG 162 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H VAL* 3.6 60.2 + - + +
134H ARG* 2.9 32.0 + - - +
136H SER* 5.9 0.9 - - - +
160H VAL 4.0 0.2 + - - -
161H PRO* 1.3 75.7 - - - +
163H LEU* 1.3 74.6 + - - +
181H PHE* 3.7 41.7 - - + +
182H CYS 3.7 12.6 - - - +
183H ALA* 4.1 4.5 - - + -
199H HIS* 4.8 9.1 - - + +
201H THR* 5.8 0.2 + - - -
210H THR* 4.4 16.8 + - - +
230H ARG* 3.0 41.4 - - - +
232H SER* 5.6 0.6 + - - -
45T TRP* 5.3 3.8 + - - -
91T GLU* 4.6 3.0 + - - -
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Residues in contact with LEU 163 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161H PRO* 3.7 16.6 - - + +
162H ARG* 1.3 90.9 + - - +
164H MET* 1.3 69.4 + - - +
165H THR 3.7 1.0 + - - -
167H ASP* 4.1 7.2 - - + -
168H CYS* 3.9 24.0 - - + +
170H GLN* 3.9 15.0 - - - +
181H PHE* 4.6 5.0 - - - +
182H CYS* 3.0 27.1 + - + +
183H ALA* 4.7 0.2 - - - -
184H GLY 4.4 2.9 - - - +
225H PHE* 3.5 50.9 - - + -
91T GLU* 4.7 1.4 - - - +
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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