Contacts of the strand formed by residues 24 - 32 (chain J) in PDB entry 4M75
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 ARG 24 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163H VAL* 5.0 0.5 - - - +
18I GLU* 2.8 21.4 + - - -
22I ASP* 3.4 21.8 + - - +
68I ARG* 2.6 38.9 - - - +
69I TYR* 3.7 22.2 + - - +
19J LYS* 4.0 2.9 - - - +
20J LEU* 3.1 35.5 + - + +
21J ARG 5.6 0.2 - - - +
22J GLY* 3.1 22.4 + - - +
23J ALA* 1.3 76.9 - - - +
25J THR* 1.3 64.9 + - - +
46J GLU* 3.8 8.5 + - - +
47J THR 3.2 12.6 - - - +
48J ILE* 3.6 39.7 - - + +
49J TYR* 5.6 1.7 - - - -
61J ARG* 5.3 6.5 - - - +
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Residues in contact with THR 25 (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 TYR* 3.4 36.0 + - + +
18J ILE 3.5 5.0 + - - -
19J LYS* 3.9 13.0 - - - +
20J LEU* 4.5 1.3 - - - +
24J ARG* 1.3 79.0 + - - +
26J LEU* 1.3 64.2 + - - +
27J VAL* 5.4 3.1 - - + +
46J GLU* 3.2 2.8 - - - +
47J THR* 2.5 64.2 + - + +
49J TYR* 5.0 15.5 + - - +
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Residues in contact with LEU 26 (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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69I TYR* 4.4 6.3 - - + +
16J VAL 4.0 0.3 - - - +
17J TYR* 4.1 1.3 - - - -
18J ILE* 2.7 48.6 + - + +
20J LEU* 3.8 22.8 - - + +
25J THR* 1.3 80.1 - - - +
27J VAL* 1.3 63.9 + - - +
41J LEU* 2.4 40.2 - - + -
44J ALA* 3.8 14.8 - - + -
45J VAL 3.7 4.0 - - - +
46J GLU* 3.8 15.5 - - + -
66J VAL* 5.1 3.4 - - + -
68J ILE* 2.4 42.2 - - + -
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Residues in contact with VAL 27 (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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15J ARG* 4.0 16.8 + - + +
16J VAL 3.5 16.6 - - - +
17J TYR* 5.1 9.6 - - + -
25J THR* 5.9 2.7 - - + -
26J LEU* 1.3 81.0 - - - +
28J GLY* 1.3 59.7 + - - +
43J ASP 4.0 0.2 - - - +
44J ALA* 3.1 2.0 - - - +
45J VAL* 2.6 80.5 + - + +
47J THR* 5.7 3.6 - - - +
79J PRO* 4.9 11.9 - - + -
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Residues in contact with GLY 28 (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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15J ARG* 3.0 22.9 - - - -
16J VAL* 3.1 23.5 + - - +
27J VAL* 1.3 81.2 - - - +
29J THR* 1.3 59.8 + - - -
30J LEU 2.9 9.4 + - - -
41J LEU* 3.9 10.3 - - - +
42J SER 3.5 1.1 - - - -
43J ASP 3.4 4.7 - - - -
44J ALA* 3.8 7.4 - - - -
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Residues in contact with THR 29 (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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13J ASP* 3.9 14.4 + - - -
14J GLU 3.9 12.1 - - - -
15J ARG* 3.2 18.4 - - - +
28J GLY* 1.3 66.8 - - - -
30J LEU* 1.3 56.4 + - - +
31J GLN* 2.4 31.4 + - - -
41J LEU* 4.4 0.4 - - - -
42J SER* 2.4 55.4 + - - +
43J ASP* 3.1 30.5 - - + +
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Residues in contact with LEU 30 (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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8J LEU* 3.6 32.3 - - + +
11J ASN* 4.0 21.8 - - + +
12J LEU* 4.0 12.3 - - + -
13J ASP* 3.0 20.5 + - - -
14J GLU 3.3 16.1 + - - +
16J VAL* 3.9 15.3 - - + -
18J ILE* 6.0 0.4 - - + -
28J GLY 2.9 6.5 + - - -
29J THR* 1.3 70.5 - - - +
31J GLN* 1.3 73.4 + - - +
32J ALA 3.8 9.6 - - - +
33J PHE* 4.5 10.1 - - + -
39J ILE* 3.4 34.1 - - + -
41J LEU* 3.7 9.6 - - + -
76J ILE* 6.1 2.2 - - + -
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Residues in contact with GLN 31 (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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79I THR* 3.2 27.5 - - + +
82I LEU* 4.1 3.7 - - + +
83I GLN* 1.9 55.9 + - - +
86I THR* 3.4 8.1 + - - -
12J LEU* 3.7 9.8 - - - +
13J ASP* 3.9 3.3 - - - +
29J THR* 2.4 27.6 + - - -
30J LEU* 1.3 100.4 + - - +
32J ALA* 1.3 65.3 + - + +
40J VAL* 2.9 28.4 + - + +
42J SER* 2.5 21.3 + - - +
65J MSE 4.7 9.0 - - + -
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Residues in contact with ALA 32 (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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2I LEU* 4.2 7.6 - - + -
3I PHE* 4.2 1.6 - - + -
82I LEU* 3.5 25.6 - - + -
86I THR* 3.2 21.1 - - + +
12J LEU* 4.5 0.9 - - - -
30J LEU* 4.1 1.5 - - - +
31J GLN* 1.3 82.2 - - - +
33J PHE* 1.3 62.4 + - - +
39J ILE* 3.1 25.3 - - - +
40J VAL* 3.1 21.5 + - + -
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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