Contacts of the strand formed by residues 102 - 108 (chain A) in PDB entry 2G5W
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 PHE 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A PHE* 3.6 42.0 - + + -
22A ASP* 3.6 26.2 - - + -
23A LEU* 3.7 19.1 - - + -
57A GLY* 3.7 16.8 - - - -
58A GLY 2.7 16.1 + - - +
59A PHE* 3.6 22.0 - - + -
60A LEU* 2.7 37.7 + - - +
96A VAL* 4.2 0.4 - - - -
97A HIS* 5.6 0.4 - + - -
100A GLY 4.5 4.7 - - - -
101A GLY* 1.3 77.0 - - - -
103A ILE* 1.3 57.6 + - - +
181A ASP* 3.2 17.0 - - + +
159B SER* 5.8 9.0 - - - -
163B ARG* 5.9 0.2 - - - -
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Residues in contact with ILE 103 (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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50A TYR* 4.0 32.3 - - + -
60A LEU* 3.3 13.9 - - + +
62A SER* 4.5 6.3 - - - +
89A TRP* 5.7 0.4 - - + -
92A VAL* 4.9 7.6 - - + -
93A VAL* 4.0 29.2 - - + -
96A VAL* 4.0 31.0 - - + -
97A HIS* 4.2 0.9 - - + -
102A PHE* 1.3 76.0 - - - +
104A PHE* 1.3 75.1 + - - +
180A PHE* 3.7 21.9 - - + -
181A ASP* 2.7 44.3 + - - +
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Residues in contact with PHE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A MET* 4.1 3.4 - - + -
21A PHE* 3.8 22.2 - + - -
59A PHE* 3.4 33.7 - + + -
60A LEU 3.0 8.4 + - - +
61A ILE* 3.6 5.9 - - + +
62A SER* 2.8 28.1 + - - -
103A ILE* 1.3 78.0 - - - +
105A CYS* 1.3 61.5 + - - +
106A GLN 3.6 0.3 + - - -
180A PHE* 3.9 2.5 - - - -
181A ASP* 3.5 9.4 - - + -
182A GLY* 3.4 28.0 - - - -
183A ILE* 3.3 26.2 - - - +
184A GLU 4.5 1.6 - - - +
234A LYS 3.5 25.1 - - - -
236A GLY 4.1 2.0 - - - -
276A ALA* 3.9 19.5 - - + -
277A TYR* 4.0 18.2 - + - +
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Residues in contact with CYS 105 (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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62A SER* 3.2 6.5 - - - -
65A THR* 3.5 39.3 - - - -
80A ILE* 4.4 6.7 - - - -
89A TRP* 4.9 1.1 - - - -
104A PHE* 1.3 69.9 - - - +
106A GLN* 1.3 63.7 + - - +
107A LEU* 3.4 12.9 + - - +
175A ALA* 4.3 8.5 - - + -
180A PHE* 3.5 39.4 - - + -
182A GLY 3.1 10.3 + - - +
183A ILE* 3.2 10.0 - - + +
184A GLU 3.0 18.8 + - - -
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Residues in contact with GLN 106 (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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31A PRO* 3.3 8.0 - - - +
61A ILE* 4.2 6.9 - - + +
62A SER* 3.0 23.8 + - - +
63A GLU 4.1 2.7 - - - +
64A GLY* 3.8 7.4 - - - -
65A THR* 2.8 34.3 + - - -
104A PHE 3.6 2.8 + - - -
105A CYS* 1.3 70.4 - - - +
107A LEU* 1.3 61.3 + - - +
184A GLU* 2.5 41.9 + - - +
186A HIS* 3.0 33.8 - - + +
238A ARG* 4.2 2.4 - - - +
401A FMN 2.5 45.7 + - - +
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Residues in contact with LEU 107 (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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65A THR 3.8 1.8 - - - +
67A VAL* 3.7 10.3 - - + -
80A ILE* 4.0 16.8 - - + -
105A CYS* 4.0 17.3 - - - +
106A GLN* 1.3 70.2 - - - +
108A TRP* 1.3 58.9 + - - +
109A HIS 4.3 0.3 + - - -
168A TYR* 3.5 49.1 - - + +
171A SER* 3.9 21.5 - - - +
172A ALA* 3.8 16.4 - - + +
175A ALA* 5.1 0.2 - - + -
183A ILE* 4.0 29.4 - - + -
184A GLU 2.8 13.6 + - - +
185A ILE* 4.3 4.0 - - + -
186A HIS* 3.3 23.8 + - - +
226A VAL* 4.6 0.7 - - + -
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Residues in contact with TRP 108 (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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33A THR* 3.0 31.2 - - + -
64A GLY* 3.4 28.5 - - - -
65A THR 2.8 30.7 + - - +
66A MET* 3.8 2.4 - - + -
67A VAL* 3.7 8.3 - - - +
71A SER* 3.5 21.6 + - - +
72A ALA* 6.3 0.9 - - - -
73A GLY 5.8 0.9 - - - -
74A PHE* 3.6 24.9 - + + -
77A VAL* 4.4 15.5 - - + -
107A LEU* 1.3 74.7 - - - +
109A HIS* 1.3 76.2 + - - +
110A VAL* 3.6 18.0 - - + +
168A TYR* 4.5 0.2 - - - -
186A HIS* 3.3 27.7 - + + -
191A TYR* 3.3 51.9 - + + -
401A FMN 4.1 1.1 - - - -
402A 8PG 4.2 6.1 - + - -
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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