Contacts of the strand formed by residues 46 - 52 (chain A) in PDB entry 4J84
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40A TRP* 3.6 6.5 - - - -
41A ASN* 2.9 30.5 + - + +
44A THR* 3.3 24.8 + - - +
45A GLN* 1.3 83.1 - - - +
47A GLU* 1.3 74.4 + - - +
48A VAL* 3.5 0.5 + - - +
14B ASP* 5.8 0.9 - - - +
271B GLU* 5.7 1.3 - - - +
293B ASN* 3.7 33.7 - - - +
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Residues in contact with GLU 47 (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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36A ARG* 3.0 27.4 + - - -
38A GLU* 3.5 20.8 - - + +
39A ILE 3.5 10.3 - - - +
40A TRP* 3.4 37.0 - - + +
46A VAL* 1.3 84.5 - - - +
48A VAL* 1.3 63.4 + - - +
49A ARG* 4.6 4.9 - - - +
50A SER* 3.6 6.3 - - - -
13B SER* 4.0 3.2 + - - -
14B ASP* 3.1 49.4 + - - +
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Residues in contact with VAL 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27A TRP* 3.5 57.2 - - + +
39A ILE* 2.7 27.3 + - + +
41A ASN* 3.9 19.3 - - + +
46A VAL 4.4 0.2 - - - +
47A GLU* 1.3 73.6 - - - +
49A ARG* 1.3 68.0 + - + +
84A TYR 4.9 7.6 - - - +
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Residues in contact with ARG 49 (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 ILE* 2.8 40.6 + - + +
47A GLU* 3.5 4.3 - - - +
48A VAL* 1.3 85.8 + - + +
50A SER* 1.3 72.5 + - - +
51A ILE* 4.4 15.5 - - + -
82A PHE* 6.2 0.2 - - - -
83A ASN 4.6 0.2 - - - -
84A TYR* 3.0 30.1 + - - +
85A ASN 3.0 28.1 + - - -
86A THR* 3.5 8.7 + - - +
87A GLY* 3.6 28.5 - - - +
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Residues in contact with SER 50 (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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36A ARG* 3.0 37.3 + - - -
37A VAL* 3.2 14.4 - - - -
38A GLU* 4.1 1.6 - - - -
47A GLU* 3.6 11.3 + - - -
49A ARG* 1.3 80.9 - - - +
51A ILE* 1.3 69.4 + - - +
14B ASP* 3.9 12.9 + - - -
34B SER* 5.3 3.6 - - - -
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Residues in contact with ILE 51 (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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36A ARG* 3.4 6.4 - - - +
37A VAL* 2.9 47.7 + - + -
49A ARG* 4.4 20.4 - - + -
50A SER* 1.3 81.2 - - - +
52A GLN* 1.3 71.4 + - - +
53A VAL* 3.2 13.4 + - + +
70A ILE* 4.6 4.7 - - + -
82A PHE* 3.7 51.1 - - + -
87A GLY* 5.2 3.6 - - - +
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Residues in contact with GLN 52 (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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34A SER* 3.0 21.1 + - - -
35A GLY 3.5 6.2 - - - -
36A ARG* 3.6 18.2 - - - +
51A ILE* 1.3 77.1 - - - +
53A VAL* 1.3 61.6 + - - +
54A THR 2.9 24.5 + - - +
55A GLU* 3.9 23.1 + - - +
36B ARG* 4.2 13.7 + - - -
52B GLN* 3.8 44.1 + - + +
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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