Contacts of the strand formed by residues 163 - 171 (chain C) in PDB entry 2A4R
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 VAL 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129C PRO* 3.6 27.1 - - + +
130C ARG 3.4 18.8 - - - +
131C PRO* 4.2 2.2 - - + -
159C CYS* 3.1 2.0 - - - -
160C THR 2.9 40.3 + - - +
161C ARG* 3.4 3.3 - - + +
162C GLY* 1.3 77.9 - - - +
164C ALA* 1.3 61.4 + - - +
165C LYS* 3.5 20.5 + - - +
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Residues in contact with ALA 164 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126C LEU* 3.7 3.6 - - + +
129C PRO* 3.1 6.2 - - - +
130C ARG 2.6 37.6 + - - +
132C ILE* 4.2 9.5 - - - +
135C LEU* 3.9 31.4 - - + -
157C ALA* 4.2 12.6 - - + -
158C VAL 3.7 2.2 - - - +
159C CYS* 3.5 16.4 - - + +
162C GLY 4.0 1.0 + - - -
163C VAL* 1.3 70.3 - - - +
165C LYS* 1.3 60.0 + - - +
166C ALA 4.5 2.2 - - - +
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Residues in contact with LYS 165 (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 SER* 3.5 7.3 - - - -
126C LEU* 2.9 28.4 + - - +
129C PRO* 3.8 28.5 - - + -
158C VAL 3.2 5.9 + - - +
160C THR* 3.9 35.3 + - - +
163C VAL* 3.5 20.4 + - + +
164C ALA* 1.3 76.9 - - - +
166C ALA* 1.3 63.6 + - + +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C ARG* 4.2 12.6 - - + +
124C GLY 3.2 16.2 - - - +
125C SER* 4.1 4.7 - - - +
126C LEU* 4.3 1.5 - - - +
157C ALA* 3.7 3.5 - - - +
158C VAL* 2.8 47.1 + - + +
164C ALA* 3.6 2.8 - - - +
165C LYS* 1.3 84.2 + - + +
167C VAL* 1.3 67.5 + - - +
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Residues in contact with VAL 167 (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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106C LEU* 4.4 7.6 - - + -
116C VAL* 4.3 19.3 - - + -
123C ARG* 3.1 23.0 - - - -
124C GLY* 2.9 28.2 + - - +
126C LEU* 4.0 10.1 - - + -
135C LEU* 3.9 19.5 - - + -
143C LEU* 4.5 18.8 - - + -
154C PHE* 3.5 28.5 - - + -
156C ALA 3.5 4.7 - - - -
157C ALA* 4.6 0.4 - - - -
158C VAL* 4.2 2.7 - - - +
166C ALA* 1.3 81.2 - - - +
168C ASP* 1.3 60.1 + - - +
169C PHE* 4.6 7.1 - - + -
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Residues in contact with ASP 168 (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 SER* 3.2 18.8 + - - +
123C ARG* 3.4 25.1 + - - -
154C PHE* 3.7 4.7 - - - -
155C ARG* 2.8 51.7 + - + +
156C ALA* 2.6 27.4 + - + +
158C VAL* 4.3 6.3 - - + +
167C VAL* 1.3 72.9 - - - +
169C PHE* 1.3 62.7 + - - +
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Residues in contact with PHE 169 (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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104C LEU* 3.9 22.0 - - + -
118C ARG* 3.4 32.3 - - - -
120C GLY 4.0 0.4 - - - -
121C ASP 3.3 19.3 - - - -
122C SER* 3.0 39.9 + - - -
123C ARG 3.8 26.2 - - - -
124C GLY* 4.5 0.7 - - - -
143C LEU* 4.0 23.1 - - + -
151C VAL* 4.1 10.8 - - + -
152C GLY* 3.9 7.4 - - - -
153C LEU 3.3 17.7 - - - +
155C ARG* 3.7 5.8 - - - +
167C VAL* 4.6 6.5 - - + -
168C ASP* 1.3 77.6 - - - +
170C ILE* 1.3 66.0 + - - +
171C PRO* 3.4 15.5 - - + +
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Residues in contact with ILE 170 (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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55C VAL* 4.5 5.8 - - + -
80C GLN* 3.4 30.1 - - + +
81C ASP 3.8 16.6 - - - +
82C LEU* 4.3 14.6 - - + -
152C GLY* 3.0 0.3 - - - -
153C LEU* 2.8 52.8 + - + +
155C ARG* 3.5 23.6 - - + -
169C PHE* 1.3 72.6 - - - +
171C PRO* 1.3 68.7 - - + +
174C ASN* 3.8 27.6 - - + +
175C LEU* 3.9 12.3 - - + +
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Residues in contact with PRO 171 (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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118C ARG* 4.5 4.0 - - - +
121C ASP* 3.0 33.2 - - + +
122C SER* 4.5 3.8 - - - -
151C VAL 3.5 8.7 - - - +
152C GLY* 4.0 1.1 - - - -
169C PHE* 3.4 11.7 - - + +
170C ILE* 1.3 86.8 - - + +
172C VAL* 1.3 64.7 + - - +
173C GLU* 3.1 20.6 - - + +
174C ASN* 2.9 42.9 + - - +
175C LEU* 3.5 3.8 - - - +
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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