Contacts of the strand formed by residues 59 - 66 (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 59 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B MET* 3.6 21.8 - - + -
21B PHE* 5.4 0.4 - + - -
23B LEU* 4.0 20.5 - - + +
25B HIS* 4.9 1.2 + - - -
27B VAL 4.2 6.2 + - - +
28B VAL* 3.4 36.5 - - + +
29B LEU 3.2 20.3 + - - -
57B GLY 4.1 0.8 + - - -
58B GLY* 1.3 72.8 - - - -
60B LEU* 1.3 63.2 + - - +
61B ILE* 3.7 21.3 - - + -
102B PHE* 3.4 25.6 - - + -
104B PHE* 3.4 50.0 - + + -
277B TYR* 3.7 23.6 - + - -
318B MET* 3.9 6.3 - - + -
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Residues in contact with LEU 60 (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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29B LEU* 3.6 33.7 - - + +
50B TYR* 4.2 9.9 - - + +
53B ARG 3.5 24.9 - - - +
54B THR* 3.5 32.5 - - + -
55B THR 5.4 0.2 - - - +
58B GLY 4.7 4.7 - - - +
59B PHE* 1.3 84.6 - - - +
61B ILE* 1.3 66.7 + - - +
96B VAL* 3.8 23.1 - - + -
102B PHE 2.6 15.2 + - - +
103B ILE* 3.3 14.9 - - + -
104B PHE 3.0 24.5 + - - -
346B PHE* 5.2 1.6 - - + -
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Residues in contact with ILE 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B VAL* 3.9 8.1 - - + -
29B LEU* 3.0 24.8 + - - +
30B ALA* 3.9 2.6 - - - +
31B PRO* 3.3 34.5 - - + +
32B MET 4.6 0.3 + - - -
50B TYR* 4.4 1.5 - - - -
59B PHE* 3.7 15.7 - - + -
60B LEU* 1.3 77.2 - - - +
62B SER* 1.3 67.7 + - - +
103B ILE* 4.9 2.0 - - - -
104B PHE* 3.8 8.3 - - + +
106B GLN* 4.2 3.8 - - + -
184B GLU* 3.6 32.8 - - + +
277B TYR* 3.5 15.9 - - - +
279B HIS* 3.6 22.0 - - + -
318B MET* 3.7 15.9 - - + -
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Residues in contact with SER 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B PRO* 3.1 20.0 - - - +
50B TYR* 3.5 15.9 - - - -
60B LEU 4.3 0.2 - - - -
61B ILE* 1.3 74.9 - - - +
63B GLU* 1.3 71.5 + - - +
65B THR* 3.8 4.0 + - - -
89B TRP* 4.5 11.0 - - - -
103B ILE* 4.1 13.4 - - - +
104B PHE 3.0 14.3 + - - -
105B CYS* 3.1 8.2 - - - +
106B GLN* 2.9 31.5 + - - +
180B PHE* 4.4 5.2 - - - -
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Residues in contact with GLU 63 (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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32B MET 3.2 35.7 - - - +
33B THR* 4.0 5.6 - - - +
34B ARG* 4.5 11.2 + - - +
35B CYS 4.6 5.4 + - - -
36B ARG 5.0 0.3 + - - -
37B ALA* 4.5 2.4 + - - +
46B LEU* 3.6 20.8 - - - +
49B TYR* 4.9 1.4 - - - -
50B TYR* 2.7 39.2 + - - +
62B SER* 1.3 77.6 + - - +
64B GLY* 1.3 61.8 + - - +
65B THR* 2.8 23.0 + - - -
77B VAL* 5.8 0.6 - - + +
78B PRO* 3.4 37.1 - - + +
89B TRP* 4.5 5.6 - - + -
106B GLN 3.8 0.9 - - - +
379B TYR* 4.0 6.0 + - - -
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Residues in contact with GLY 64 (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* 4.1 1.5 + - - -
63B GLU* 1.3 71.6 - - - +
65B THR* 1.3 60.3 + - - -
77B VAL* 4.3 4.7 - - - +
78B PRO* 4.0 13.5 - - - +
106B GLN* 3.2 25.7 + - - -
108B TRP* 3.3 35.6 - - - -
403B FMN 3.2 13.3 + - - -
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Residues in contact with THR 65 (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* 3.8 0.7 + - - -
63B GLU 2.8 15.4 + - - -
64B GLY* 1.3 73.3 - - - -
66B MET* 1.3 66.3 + - - +
78B PRO* 3.4 12.1 - - - +
79B GLY 3.3 30.3 - - - +
80B ILE* 3.6 14.6 - - + +
89B TRP* 3.7 19.1 - - + -
105B CYS* 3.6 17.9 - - - -
106B GLN 2.6 15.2 + - - +
107B LEU* 3.7 2.4 - - - -
108B TRP* 2.7 33.9 + - - +
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Residues in contact with MET 66 (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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40B GLY* 3.9 8.3 - - - -
65B THR* 1.3 71.6 - - - +
67B VAL* 1.3 59.2 + - - +
68B SER 4.4 4.5 - - - +
69B PRO* 5.6 1.8 - - - -
70B GLY 5.7 0.9 - - - -
71B SER* 3.3 17.0 - - - +
72B ALA* 3.5 32.1 - - + -
77B VAL* 3.4 28.5 - - + +
78B PRO 2.7 13.3 + - - +
79B GLY* 3.5 18.6 - - - +
80B ILE* 2.9 29.5 + - - +
81B TYR* 3.6 28.7 + - + +
85B GLN* 3.9 8.1 - - - +
108B TRP* 3.9 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