Contacts of the strand formed by residues 15 - 20 (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 15 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11J ASN* 4.6 3.1 - - - +
14J GLU* 1.3 82.6 - - - +
16J VAL* 1.3 65.5 + - - +
27J VAL* 4.0 21.2 + - + +
28J GLY* 3.0 21.8 - - - -
29J THR* 3.2 17.9 - - - +
43J ASP* 2.3 43.4 + - - +
45J VAL* 4.5 8.7 - - - +
78J THR* 4.6 2.4 - - - +
79J PRO* 3.8 23.2 - - + +
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Residues in contact with VAL 16 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8J LEU* 6.3 0.7 - - + -
11J ASN* 3.8 28.3 - - + +
14J GLU 3.5 7.6 - - - +
15J ARG* 1.3 85.7 - - - +
17J TYR* 1.3 60.9 + - - +
18J ILE* 3.9 10.7 + - + -
26J LEU 4.0 0.2 - - - +
27J VAL* 3.5 26.3 - - - +
28J GLY 3.1 20.0 + - - +
30J LEU* 3.9 25.1 - - + +
41J LEU* 4.3 9.9 - - + -
76J ILE* 4.2 14.4 - - + -
77J SER 4.0 4.0 - - - +
78J THR* 5.6 0.2 - - - -
79J PRO* 3.9 10.7 - - - +
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Residues in contact with TYR 17 (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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16J VAL* 1.3 74.1 - - - +
18J ILE* 1.3 63.3 + - - +
19J LYS* 4.1 24.3 - - + +
25J THR* 3.4 36.0 + - + +
26J LEU 4.1 4.0 - - - -
27J VAL* 5.0 8.5 - - + +
49J TYR* 5.4 3.1 + - - -
75J LEU* 3.6 8.4 - - + +
76J ILE* 3.1 28.1 - - - +
77J SER* 2.7 23.5 + - - +
78J THR 4.7 0.9 - - - +
79J PRO* 4.2 16.4 - - + +
67K PHE* 4.1 31.6 - + - -
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Residues in contact with ILE 18 (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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16J VAL* 4.6 7.6 - - + -
17J TYR* 1.3 82.3 - - - +
19J LYS* 1.3 60.7 + - - +
20J LEU* 3.0 34.9 + - + -
25J THR* 3.5 4.2 + - - +
26J LEU* 2.7 52.6 + - + +
30J LEU* 6.0 0.4 - - + -
39J ILE* 3.4 31.9 - - + -
41J LEU* 4.2 16.6 - - + -
68J ILE* 3.9 18.2 - - + -
73J VAL* 4.5 9.4 - - + -
75J LEU 3.7 2.2 - - - -
76J ILE* 4.0 14.4 - - + -
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Residues in contact with LYS 19 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161H GLY 2.9 29.0 + - - -
162H ILE* 4.9 1.8 - - - +
163H VAL* 4.7 13.0 - - + -
17J TYR* 4.1 18.8 - - + +
18J ILE* 1.3 72.5 - - - +
20J LEU* 1.3 62.7 + - - +
24J ARG 4.4 2.5 - - - +
25J THR* 3.9 14.1 - - - +
74J THR* 2.7 38.5 + - + -
75J LEU* 2.8 37.7 + - + +
32K LEU* 3.5 11.6 - - - +
34K TYR* 3.1 6.5 + - - +
54K GLU* 2.4 36.5 + - - +
67K PHE* 5.8 1.6 - - + -
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Residues in contact with LEU 20 (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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163H VAL* 2.7 25.6 - - - +
68I ARG* 5.6 2.9 - - + -
69I TYR* 3.3 31.6 - - + +
18J ILE* 3.0 32.8 - - + +
19J LYS* 1.3 72.6 - - - +
21J ARG* 1.3 65.8 + - - +
22J GLY 3.1 2.3 + - - -
24J ARG* 3.1 33.5 + - + +
26J LEU* 3.8 23.6 - - + -
68J ILE* 4.1 11.7 - - + -
72J THR* 3.6 11.9 - - + +
73J VAL* 3.8 24.7 - - + +
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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