Contacts of the strand formed by residues 173 - 180 (chain e) in PDB entry 5GJQ
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 ALA 173 (chain e).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16e ALA 3.4 1.7 - - - +
17e ASP* 3.2 24.9 - - - -
18e SER* 2.8 17.1 + - - +
29e GLN 4.8 3.6 - - - +
171e GLY 3.3 0.8 + - - -
172e GLY* 1.3 76.5 - - - +
174e VAL* 1.3 65.3 + - - +
175e ASN* 3.8 13.0 + - - +
189e SER* 5.0 4.5 - - - +
190e ASP 3.3 15.5 - - - +
191e ASN* 4.1 9.6 - - - +
192e VAL* 4.2 3.1 - - - +
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Residues in contact with VAL 174 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15e ALA* 5.0 2.5 - - + -
16e ALA 3.6 2.9 - - - +
157e ARG* 4.1 24.4 + - + -
160e ILE* 3.6 41.1 - - + -
161e TYR 4.6 5.6 - - - +
164e THR* 5.2 0.2 - - + -
173e ALA* 1.3 74.5 - - - +
175e ASN* 1.3 70.0 + - - +
176e LEU* 4.2 3.8 + - + -
188e SER* 3.9 2.3 + - - +
189e SER* 3.5 2.3 - - - -
190e ASP* 2.8 34.6 + - - +
192e VAL* 4.0 15.3 - - + -
195e LEU* 3.6 28.7 - - + -
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Residues in contact with ASN 175 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14e VAL 3.9 0.5 - - - +
15e ALA* 3.3 6.9 - - - +
16e ALA* 3.0 36.6 + - + +
17e ASP 5.2 0.8 + - - -
18e SER* 4.3 11.3 - - - -
31e VAL 5.2 3.2 + - - -
34e VAL* 5.1 3.0 - - + +
173e ALA* 3.9 20.8 + - - +
174e VAL* 1.3 75.0 - - - +
176e LEU* 1.3 61.5 - - - +
177e TYR* 4.7 16.0 - - + -
186e ARG* 5.8 5.6 - - + +
188e SER 3.5 3.0 - - - +
189e SER* 2.7 31.9 + - - -
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Residues in contact with LEU 176 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13e ILE* 3.4 24.7 - - + -
14e VAL 3.2 17.5 - - - +
15e ALA* 3.6 15.0 - - + -
153e TYR* 3.6 37.0 - - + +
156e ALA* 4.0 2.7 - - + -
157e ARG* 3.6 34.1 - - + +
174e VAL* 5.0 4.7 - - + +
175e ASN* 1.3 76.1 - - - +
177e TYR* 1.3 67.1 + - - +
186e ARG* 3.8 2.6 - - - +
187e VAL* 2.8 28.9 + - + -
188e SER* 2.9 27.1 + - - +
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Residues in contact with TYR 177 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13e ILE* 3.6 9.0 - - - +
14e VAL* 2.9 36.2 + - + +
32e LYS* 4.2 8.7 + - - +
34e VAL* 3.5 46.8 + - + +
36e GLU* 2.9 33.3 + - + -
42e LEU* 3.8 27.8 - - + -
175e ASN* 4.8 8.5 - - + -
176e LEU* 1.3 85.8 - - - +
178e HIS* 1.3 62.2 + - - +
184e TRP* 4.0 20.6 - + - -
185e ILE 3.5 9.0 - - - -
186e ARG* 3.4 28.9 + - + -
187e VAL* 4.1 2.9 - - - -
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Residues in contact with HIS 178 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8e PHE* 4.4 3.0 - + - -
10e HIS* 2.9 28.4 + - + -
11e GLY* 4.2 0.6 - - - -
12e VAL 3.7 4.3 - - - -
13e ILE* 3.9 15.4 - - + +
149e VAL* 4.3 19.5 - - + -
153e TYR* 2.5 42.3 + + + +
177e TYR* 1.3 76.0 - - - +
179e VAL* 1.3 84.4 + - - +
180e ARG* 3.5 27.2 + - + +
183e GLY 4.1 0.2 - - - +
184e TRP* 3.0 5.0 - - - -
185e ILE* 2.8 38.9 + - + +
187e VAL* 3.5 9.6 - - + -
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Residues in contact with VAL 179 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11e GLY* 3.1 9.5 - - - -
12e VAL* 2.7 54.3 + - + +
14e VAL* 5.0 0.4 - - + -
40e TYR 5.5 2.7 - - - +
42e LEU* 3.9 28.5 - - + -
102e CYS* 4.5 6.3 - - + +
103e GLY* 3.6 40.6 - - - +
104e TRP* 3.7 8.0 - - + +
178e HIS* 1.3 73.1 - - - +
180e ARG* 1.3 66.3 + - - +
183e GLY 5.5 0.9 - - - -
184e TRP* 3.9 11.9 - - + -
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Residues in contact with ARG 180 (chain e).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10e HIS* 4.2 4.9 - - - +
104e TRP* 3.2 18.0 - - + +
153e TYR* 5.2 1.0 + - - -
178e HIS* 3.5 43.0 + - + +
179e VAL* 1.3 74.1 - - - +
181e GLU* 1.3 67.6 + - - +
182e ASP* 3.0 43.6 + - - +
183e GLY* 2.8 29.0 + - - +
185e ILE* 4.1 22.7 - - - +
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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