Contacts of the strand formed by residues 57 - 63 (chain A) in PDB entry 2GJD
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 VAL 57 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A GLY* 4.5 8.7 - - - +
25A TYR* 3.8 31.6 + - + +
44A GLY* 4.1 2.5 - - - -
45A ILE 3.5 18.2 - - - +
46A PRO* 4.3 11.9 - - + -
55A GLY 4.8 4.5 - - - +
56A GLY* 1.3 78.1 - - - +
58A TYR* 1.3 61.6 + - - +
59A PRO* 3.6 6.1 - - - +
155A TYR* 3.0 25.2 + - - +
157A LYS* 4.7 22.0 - - + +
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Residues in contact with TYR 58 (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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44A GLY* 3.5 1.1 - - - -
45A ILE* 2.8 55.2 + - + +
47A GLY* 3.8 8.7 - - - -
53A TRP* 2.7 55.0 + + - -
56A GLY* 3.7 14.3 - - - -
57A VAL* 1.3 71.4 - - - +
59A PRO* 1.3 70.3 - - + +
60A ILE 3.7 0.9 + - - -
77A PHE* 3.6 22.7 - - + -
81A PHE* 3.6 23.3 - + + -
120A LEU* 3.9 13.2 - - + -
151A GLN* 4.0 12.8 - - + -
152A ALA* 3.2 21.0 - - - +
155A TYR* 3.7 27.8 - + + -
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Residues in contact with PRO 59 (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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25A TYR* 4.2 10.8 - - - +
43A ALA 3.4 10.1 - - - +
44A GLY* 4.3 2.2 - - - -
57A VAL 3.6 3.8 - - - +
58A TYR* 1.3 84.5 - - + +
60A ILE* 1.3 65.7 + - - +
77A PHE* 3.5 3.2 - - + -
78A PRO* 3.4 34.8 - - + +
81A PHE* 5.4 0.2 - - + -
155A TYR* 3.5 37.0 - - + -
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Residues in contact with ILE 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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42A GLU* 3.5 5.2 - - - +
43A ALA* 2.9 59.5 + - + +
45A ILE* 3.9 22.7 - - + -
58A TYR 4.3 2.0 - - - +
59A PRO* 1.3 82.3 - - - +
61A THR* 1.3 66.8 + - - +
62A VAL* 4.1 9.9 - - + -
75A VAL* 3.8 19.3 - - + -
76A LYS 3.1 12.3 - - - +
77A PHE* 3.4 31.9 - - + -
92A ILE* 4.2 7.2 - - + -
112A ILE* 5.9 1.1 - - + -
113A VAL* 4.3 8.7 - - + -
116A VAL* 5.2 4.5 - - + -
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Residues in contact with THR 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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40A LYS* 4.6 21.5 - - - +
41A TRP 3.3 9.2 - - - +
42A GLU* 4.4 16.4 - - + +
60A ILE* 1.3 78.2 - - - +
62A VAL* 1.3 62.4 + - - +
63A GLU* 4.1 7.3 + - - -
74A LYS 3.7 0.9 - - - +
75A VAL* 3.3 6.8 - - - +
76A LYS* 2.9 51.3 + - - +
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Residues in contact with VAL 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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39A GLN 3.8 0.7 - - - +
40A LYS* 3.4 2.8 - - - -
41A TRP* 2.9 41.3 + - + +
43A ALA* 4.7 5.6 - - + -
60A ILE* 4.1 23.6 - - + -
61A THR* 1.3 77.4 - - - +
63A GLU* 1.3 59.8 + - - +
64A TYR* 3.6 27.8 + - + +
73A PRO* 3.5 31.6 - - + -
74A LYS 3.5 2.9 - - - -
75A VAL* 4.2 10.3 - - + +
109A LEU* 4.5 18.4 - - + -
112A ILE* 5.6 0.9 - - + -
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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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39A GLN 3.4 5.6 - - - +
40A LYS* 4.4 28.3 + - + +
61A THR* 4.6 8.5 + - - +
62A VAL* 1.3 76.5 - - - +
64A TYR* 1.3 62.5 + - - +
65A PRO* 3.6 2.6 - - - +
73A PRO* 3.3 2.2 - - - +
74A LYS* 2.9 56.0 + - + +
76A LYS* 3.8 23.9 - - - +
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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