Contacts of the strand formed by residues 59 - 66 (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 59 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A MET* 3.5 24.5 - - + -
21A PHE* 5.0 0.7 - + - -
23A LEU* 4.0 28.0 - - + +
25A HIS* 4.8 1.4 + - - -
27A VAL 4.0 7.1 + - - +
28A VAL* 3.6 30.0 - - + -
29A LEU 3.3 19.1 + - - -
57A GLY 3.9 1.2 + - - -
58A GLY* 1.3 71.8 - - - -
60A LEU* 1.3 69.6 + - - +
61A ILE* 3.8 17.9 - - + -
102A PHE* 3.6 22.0 - + + -
104A PHE* 3.4 42.8 - + + -
277A TYR* 3.6 27.1 - + - -
318A MET* 3.9 7.9 - - + -
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Residues in contact with LEU 60 (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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29A LEU* 3.8 31.6 - - + +
50A TYR* 3.8 16.4 - - + +
53A ARG* 3.9 20.4 - - + +
54A THR* 3.5 28.0 - - + +
55A THR 5.3 0.7 - - - +
58A GLY* 4.7 5.8 - - - +
59A PHE* 1.3 91.7 - - - +
61A ILE* 1.3 67.5 + - - +
96A VAL* 3.9 20.9 - - + -
102A PHE 2.7 18.4 + - - +
103A ILE* 3.3 9.2 - - + -
104A PHE 3.0 24.2 + - - -
346A PHE* 5.1 3.1 - - + -
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Residues in contact with ILE 61 (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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28A VAL* 4.0 3.6 - - + -
29A LEU* 3.0 30.6 + - - +
30A ALA 3.7 15.2 - - - +
31A PRO* 3.6 25.6 - - + -
32A MET 4.8 0.2 + - - -
50A TYR* 4.2 1.8 - - - -
59A PHE* 3.8 8.5 - - + -
60A LEU* 1.3 80.0 - - - +
62A SER* 1.3 67.2 + - - +
63A GLU 3.9 0.3 + - - -
104A PHE* 3.6 9.4 - - + +
106A GLN* 4.2 6.1 - - + -
184A GLU* 3.4 35.0 - - + +
277A TYR* 3.4 13.2 - - + +
279A HIS* 3.6 23.1 - - + +
318A MET* 3.8 13.2 - - + -
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Residues in contact with SER 62 (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* 3.2 16.2 - - - +
50A TYR* 3.4 17.7 - - - -
60A LEU 4.2 0.2 - - - -
61A ILE* 1.3 76.1 - - - +
63A GLU* 1.3 76.6 + - - +
65A THR* 3.6 5.2 + - - -
89A TRP* 4.4 15.3 - - - -
103A ILE* 4.5 10.8 - - - +
104A PHE 2.8 16.3 + - - -
105A CYS* 3.2 7.9 - - - -
106A GLN* 3.0 25.1 + - - +
180A PHE* 4.6 1.8 - - - -
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Residues in contact with GLU 63 (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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32A MET 3.1 36.7 - - - +
33A THR* 3.9 4.9 - - - +
34A ARG* 4.6 11.4 + - - +
35A CYS 4.6 5.9 + - - -
36A ARG 4.9 0.9 + - - -
37A ALA* 4.6 3.6 + - - +
46A LEU* 3.5 20.3 - - - +
49A TYR* 4.7 1.9 - - - -
50A TYR* 2.7 37.9 + - - +
61A ILE 3.9 0.6 + - - -
62A SER* 1.3 79.0 + - - +
64A GLY* 1.3 66.1 + - - +
65A THR* 2.9 15.9 + - - +
78A PRO* 3.2 39.1 - - + +
89A TRP* 4.7 3.8 - - + -
106A GLN 3.9 1.4 - - - +
379A TYR* 4.1 6.1 + - - -
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Residues in contact with GLY 64 (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* 4.2 1.7 + - - -
62A SER 3.7 0.6 + - - -
63A GLU* 1.3 74.3 - - - +
65A THR* 1.3 58.2 + - - -
66A MET 4.4 0.2 + - - -
77A VAL* 4.4 2.6 - - - +
78A PRO* 3.8 17.5 - - - +
106A GLN* 3.8 19.5 + - - -
108A TRP* 3.4 38.9 - - - -
401A FMN 3.4 13.5 + - - -
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Residues in contact with THR 65 (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* 3.6 2.4 + - - -
63A GLU 2.9 15.4 + - - -
64A GLY* 1.3 72.7 + - - -
66A MET* 1.3 65.8 + - - +
67A VAL* 3.9 0.5 - - - +
78A PRO* 3.4 10.4 - - - +
79A GLY 3.5 28.3 - - - +
80A ILE* 3.7 15.2 - - + +
89A TRP* 3.7 16.7 - - + +
105A CYS* 3.5 18.7 - - - -
106A GLN 2.8 17.0 + - - +
107A LEU* 3.8 2.6 - - - -
108A TRP* 2.8 32.0 + - - +
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Residues in contact with MET 66 (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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40A GLY* 4.2 8.3 - - - -
65A THR* 1.3 72.7 - - - +
67A VAL* 1.3 59.8 + - - +
68A SER 4.8 2.2 - - - +
69A PRO* 5.8 1.6 - - - -
70A GLY 5.8 0.9 - - - -
71A SER* 3.3 17.3 - - - +
72A ALA* 3.6 26.9 - - + +
77A VAL* 3.9 24.8 - - + +
78A PRO 2.8 16.1 + - - +
79A GLY* 3.7 17.7 - - - +
80A ILE* 3.1 30.0 + - - +
81A TYR* 3.5 36.6 - - + +
85A GLN* 3.8 6.1 - - - +
108A TRP* 3.8 4.9 - - + -
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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