Contacts of the strand formed by residues 77 - 82 (chain J) in PDB entry 4R2G
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 GLN 77 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E VAL* 5.0 10.1 - - - +
21J THR* 3.8 20.4 + - - +
22J CYS 3.2 15.3 - - - +
23J ILE* 4.3 16.7 - - + +
29J ILE* 3.3 12.7 - - - +
71J ARG* 3.4 0.9 - - - -
72J ASP* 2.9 40.3 + - + +
75J LYS* 3.9 35.4 - - + +
76J ASN* 1.3 77.5 - - - +
78J LEU* 1.3 62.2 + - - +
79J SER* 3.4 20.1 + - - +
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Residues in contact with LEU 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J THR* 3.1 6.9 - - - -
22J CYS* 2.9 39.8 + - + +
24J VAL* 5.7 1.3 - - + -
29J ILE* 3.9 15.0 - - + -
34J TRP* 3.4 54.1 - - + +
35J THR 4.6 0.2 - - - +
36J TRP* 3.8 24.6 - - + +
51J ILE* 3.9 10.3 - - + -
69J ILE* 4.9 1.1 - - + -
70J SER 3.6 13.2 - - - +
71J ARG* 3.9 9.9 - - + -
77J GLN* 1.3 74.0 - - - +
79J SER* 1.3 64.5 + - - +
92J CYS* 4.2 18.6 - - + -
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Residues in contact with SER 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200E VAL* 4.4 10.9 - - - +
20J VAL 3.5 3.1 - - - -
21J THR* 3.9 7.6 - - - +
36J TRP* 4.0 3.8 - - - -
68J VAL 3.4 1.4 - - - +
69J ILE* 3.3 7.8 - - - +
70J SER* 2.9 53.6 + - - +
71J ARG* 5.9 0.2 - - - -
77J GLN* 3.4 25.2 + - - +
78J LEU* 1.3 74.0 + - - +
80J LEU* 1.3 59.4 + - - +
81J GLN* 4.0 18.5 + - - +
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Residues in contact with LEU 80 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18J LEU* 6.1 2.2 - - + -
19J SER* 3.2 4.2 - - - -
20J VAL* 2.9 38.0 + - + +
36J TRP* 3.4 48.8 - - + +
48J ILE* 4.2 15.0 - - + -
67J ALA* 4.0 18.4 - - + -
68J VAL 3.5 4.0 - - - +
69J ILE* 4.3 7.4 - - + -
79J SER* 1.3 73.4 - - - +
81J GLN* 1.3 87.5 + - - +
82J LEU* 4.6 6.7 - - + -
90J TYR* 3.7 32.1 - - + -
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Residues in contact with GLN 81 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120E VAL* 3.5 38.4 - - + +
122E LEU* 4.6 1.4 - - - +
200E VAL* 2.9 33.5 - - - +
202E THR* 3.9 5.4 - - + -
17J THR* 4.6 0.7 - - + -
18J LEU 3.3 12.1 - - - +
19J SER* 3.0 20.1 + - - -
66J ARG 3.5 1.4 - - - +
67J ALA* 3.0 10.7 - - - +
68J VAL* 2.9 48.5 + - + +
70J SER* 4.5 4.5 + - - -
79J SER* 4.0 17.3 + - - +
80J LEU* 1.3 84.9 + - - +
82J LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 82 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17J THR* 3.0 9.1 - - - +
18J LEU* 2.7 50.0 + - + +
38J ARG* 3.6 5.8 - - - +
48J ILE* 4.8 3.8 - - + -
63J LEU* 4.2 20.0 - - + -
66J ARG* 3.7 10.3 - - + +
67J ALA* 3.8 29.8 - - + +
80J LEU* 4.6 9.8 - - + +
81J GLN* 1.3 74.6 - - - +
82J ARG* 1.5 68.3 - - + +
86J ASP* 3.4 22.9 - - + +
90J TYR* 3.2 35.2 - - + +
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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