Contacts of the strand formed by residues 102 - 108 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20B ARG 5.7 0.4 - - - -
21B PHE* 3.6 33.7 - + + -
22B ASP* 3.3 30.7 - - + -
23B LEU* 3.7 19.7 - - + -
57B GLY* 4.7 10.5 - - - -
58B GLY 2.9 11.5 + - - +
59B PHE* 3.4 20.9 - - + -
60B LEU* 2.6 36.2 + - - +
96B VAL* 4.1 2.0 - - - +
97B HIS* 5.0 1.3 - + - -
100B GLY 5.2 2.2 - - - -
101B GLY* 1.3 79.4 - - - -
103B ILE* 1.3 55.9 + - - +
181B ASP* 3.3 20.4 - - + +
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Residues in contact with ILE 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 4.0 33.7 - - + -
60B LEU* 3.3 19.1 - - + +
62B SER* 4.1 17.7 - - - +
89B TRP* 5.7 0.2 - - + -
92B VAL* 5.1 5.4 - - + -
93B VAL* 4.1 21.8 - - + -
96B VAL* 4.1 23.1 - - + -
97B HIS* 4.7 0.7 - - + -
102B PHE* 1.3 75.6 - - - +
104B PHE* 1.3 76.0 + - - +
180B PHE* 3.6 21.3 - - + -
181B ASP* 2.7 42.4 + - - +
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Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 4.5 0.2 - - + -
21B PHE* 3.8 25.6 - + - -
59B PHE* 3.4 35.4 - + + -
60B LEU 3.0 7.5 + - - +
61B ILE* 3.8 8.5 - - + -
62B SER* 3.0 25.8 + - - -
103B ILE* 1.3 81.5 - - - +
105B CYS* 1.3 59.8 + - - +
180B PHE* 3.7 3.1 - - - -
181B ASP* 3.7 9.0 - - + -
182B GLY* 3.1 31.0 - - - +
183B ILE* 3.3 26.7 - - - -
184B GLU 4.1 2.2 - - - +
234B LYS 3.5 16.8 - - - -
236B GLY 4.0 1.1 - - - -
276B ALA* 3.8 24.9 - - + -
277B TYR* 4.0 14.4 - + - +
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Residues in contact with CYS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62B SER* 3.1 6.1 - - - -
65B THR* 3.6 33.2 - - - -
80B ILE* 4.3 7.9 - - - -
89B TRP* 5.1 0.9 - - - -
104B PHE* 1.3 71.7 - - - +
106B GLN* 1.3 63.0 + - - +
107B LEU* 3.4 16.2 + - - +
175B ALA* 4.3 11.0 - - + -
180B PHE* 3.5 36.7 - - + -
182B GLY 3.0 7.5 + - - -
183B ILE* 3.1 10.7 - - + +
184B GLU* 2.9 20.2 + - - -
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Residues in contact with GLN 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PRO* 3.5 4.6 - - - +
61B ILE* 4.2 6.7 - - + +
62B SER* 2.9 27.4 + - - +
63B GLU 4.1 1.1 - - - +
64B GLY* 3.2 13.9 + - - -
65B THR* 2.6 35.9 + - - -
104B PHE 3.9 1.4 + - - -
105B CYS* 1.3 70.8 - - - +
107B LEU* 1.3 58.9 + - - +
184B GLU* 2.8 43.0 + - + +
186B HIS* 3.1 31.7 - - + +
238B ARG* 3.9 2.4 - - - +
403B FMN 2.6 45.7 + - - -
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Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B THR 3.8 2.7 - - - -
67B VAL* 3.6 12.8 - - + -
80B ILE* 3.8 28.9 - - + -
105B CYS* 4.1 12.6 - - - -
106B GLN* 1.3 68.7 - - - +
108B TRP* 1.3 58.5 + - - +
168B TYR* 3.9 36.7 - - + +
171B SER* 3.9 13.5 - - - +
172B ALA* 4.1 6.5 - - + -
183B ILE* 3.6 37.5 - - + -
184B GLU 2.8 14.4 + - - +
185B ILE* 3.9 11.5 - - + -
186B HIS* 3.0 27.2 + - - +
226B VAL* 4.5 0.9 - - + -
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Residues in contact with TRP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B THR* 3.0 28.7 - - + -
64B GLY* 3.3 33.0 - - - -
65B THR* 2.7 29.0 + - - +
66B MET* 3.9 3.5 - - + +
67B VAL* 4.0 5.8 + - - +
71B SER* 3.5 21.6 + - - +
72B ALA* 6.1 1.3 - - - -
73B GLY 5.6 1.1 - - - -
74B PHE* 3.5 28.5 - + + -
77B VAL* 4.6 12.8 - - + -
107B LEU* 1.3 74.1 - - - +
109B HIS* 1.3 70.2 + - - +
110B VAL* 3.6 24.2 - - + +
186B HIS* 3.4 27.3 - + + -
191B TYR* 3.4 47.2 - + + -
403B FMN 4.3 0.4 - - - -
404B 8PG 4.1 7.0 - + - -
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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