Contacts of the strand formed by residues 53 - 60 (chain A) in PDB entry 2JG1
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 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MSE 3.8 6.2 - - - +
2A ILE* 3.2 13.2 - - + +
4A THR* 3.9 16.4 - - + -
43A THR* 4.2 31.4 - - + +
46A LEU* 3.8 31.2 - - + -
47A ALA* 4.4 11.2 - - + +
51A GLU 3.7 11.9 - - - +
52A PRO* 1.3 75.6 - - - +
54A LEU* 1.3 66.3 - - - +
76A ILE* 4.8 5.6 - - + -
77A LYS* 4.1 22.9 + - - +
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Residues in contact with LEU 54 (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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1A MSE 4.1 19.3 - - + -
2A ILE 2.9 8.8 + - - +
3A LEU* 3.4 15.6 - - + +
4A THR* 3.0 25.7 + - - -
53A VAL* 1.3 76.9 - - - +
55A ALA* 1.3 62.0 + - - +
77A LYS* 3.5 19.1 - - + +
78A HIS* 3.5 39.0 - - - +
79A ALA* 3.7 4.5 - - + +
124A MSE 3.7 35.9 - - + -
127A LYS* 6.1 4.5 - - + -
128A VAL* 5.2 8.1 - - + -
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Residues in contact with ALA 55 (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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4A THR* 3.5 15.5 - - - +
40A LEU* 4.4 5.4 - - + -
43A THR* 4.1 16.7 - - + +
54A LEU* 1.3 73.0 - - - +
56A SER* 1.3 60.6 + - - +
71A LEU* 4.1 24.9 - - + -
77A LYS 2.9 14.1 + - - +
78A HIS* 3.1 3.9 - - + +
79A ALA 2.8 27.4 + - - -
80A PHE* 4.1 8.4 + - + -
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Residues in contact with SER 56 (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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3A LEU* 3.8 20.4 - - - -
4A THR 2.9 12.2 + - - +
5A LEU* 3.7 8.9 - - - -
6A THR* 3.0 23.1 + - - -
54A LEU 3.9 0.4 + - - -
55A ALA* 1.3 74.0 - - - +
57A GLY* 1.3 65.2 + - - +
79A ALA* 2.8 24.1 + - - -
80A PHE* 3.4 18.4 - - - -
117A PHE* 3.6 15.3 - - - -
120A HIS* 4.1 4.2 + - - -
124A MSE 4.7 5.6 - - - -
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Residues in contact with GLY 57 (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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6A THR 3.2 12.8 - - - -
7A LEU* 3.7 17.9 - - - -
56A SER* 1.3 82.7 + - - +
58A PHE* 1.3 63.9 + - - -
80A PHE* 3.4 5.5 - - - -
81A TYR* 2.9 28.8 + - - +
117A PHE* 3.9 7.0 - - - -
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Residues in contact with PHE 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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6A THR 3.6 5.3 + - - -
7A LEU* 3.7 39.5 - - + +
9A PRO* 3.2 28.2 - - - +
57A GLY* 1.3 73.1 - - - -
59A ILE* 1.3 61.8 + - - +
80A PHE* 4.7 0.2 - - - -
81A TYR* 3.4 16.2 - + + -
83A ILE* 3.4 28.9 - - + -
87A THR* 4.5 0.5 + - - -
107A PRO* 6.3 0.4 - - + -
109A ILE* 3.9 35.0 - - + -
113A GLU 3.9 10.5 - - - -
117A PHE* 3.6 33.9 - + + -
138A PRO* 4.4 0.7 - - + -
141A LEU* 4.3 20.0 - - + -
145A TYR* 3.8 13.0 - + - -
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Residues in contact with ILE 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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9A PRO* 4.3 11.4 - - + -
57A GLY 4.3 0.2 + - - -
58A PHE* 1.3 79.0 - - - +
60A GLY* 1.3 59.4 + - - +
64A GLY* 3.7 32.5 - - - +
65A GLN* 3.9 11.9 - - - +
67A ILE* 4.5 6.7 - - + -
68A ALA* 4.6 8.5 - - + -
78A HIS* 5.9 0.7 - - + +
80A PHE* 3.6 48.5 - - + -
81A TYR 3.1 4.7 + - - +
82A ASN* 3.4 25.6 + - - +
83A ILE* 2.9 27.8 + - - -
87A THR* 3.5 4.3 - - - +
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Residues in contact with GLY 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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59A ILE* 1.3 76.2 - - - +
61A GLY* 1.3 62.1 - - - -
63A LEU 4.1 0.7 + - - -
64A GLY* 3.1 14.9 + - - -
83A ILE* 3.8 9.6 - - - +
85A GLY 3.1 23.1 - - - -
86A GLU* 3.6 1.5 - - - +
87A THR* 2.8 30.5 + - - +
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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