Contacts of the strand formed by residues 51 - 57 (chain A) in PDB entry 1RJA
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A SER* 3.0 1.8 - - - -
44A VAL 2.5 41.0 + - - +
46A ASP* 2.9 40.0 + - + +
49A ALA* 4.9 5.3 - - + +
50A VAL* 1.3 80.7 - - - +
52A HIS* 1.3 60.5 + - - +
53A TYR* 3.1 27.1 - - + +
89A GLY* 4.4 11.5 - - - +
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Residues in contact with HIS 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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11A ARG* 4.0 19.8 - - + +
14A ALA* 3.9 11.2 - - + -
15A VAL* 3.3 23.8 - - + +
31A ARG* 3.1 28.9 + - - +
35A LYS* 5.5 5.4 - - - +
41A VAL* 5.6 1.6 - - + -
42A LEU 3.0 6.5 - - - +
43A SER* 2.9 27.6 - - - -
50A VAL* 3.3 26.7 - - + +
51A ARG* 1.3 75.2 - - - +
53A TYR* 1.3 82.4 + - - +
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Residues in contact with TYR 53 (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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41A VAL* 3.0 9.3 - - - +
42A LEU* 2.6 55.9 + - + -
44A VAL* 2.8 29.7 - - + +
46A ASP* 2.9 12.3 + - - -
51A ARG* 3.1 24.3 - - + +
52A HIS* 1.3 87.1 - - - +
54A LYS* 1.3 61.3 + - - +
55A ILE* 4.1 0.2 - - - +
65A LEU* 3.3 22.4 - - + +
87A SER 4.7 11.7 - - - -
88A HIS* 3.2 42.4 - + - -
89A GLY 4.0 5.1 + - - -
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Residues in contact with LYS 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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35A LYS* 6.2 1.8 - - - +
36A PRO* 4.0 34.5 - - + -
39A ASP* 4.6 4.9 - - + +
40A TYR 4.8 0.2 - - - +
41A VAL* 3.9 10.5 - - + -
53A TYR* 1.3 72.6 - - - +
55A ILE* 1.3 67.5 + - - +
56A TRP* 3.2 48.2 + - + +
65A LEU* 3.1 29.2 + - - +
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Residues in contact with ILE 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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30A ILE* 3.5 21.3 - - + -
39A ASP* 3.0 26.3 - - - +
40A TYR* 2.5 49.7 + - + +
41A VAL* 3.6 12.1 - - - +
42A LEU* 3.8 6.5 - - + +
54A LYS* 1.3 74.6 - - - +
56A TRP* 1.3 58.4 + - - +
63A LEU* 3.2 40.4 - - + +
64A HIS 3.8 9.6 - - - +
65A LEU* 3.7 29.2 - - + +
74A LEU* 4.1 9.2 - - + -
77A LEU* 5.9 0.2 - - + -
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Residues in contact with TRP 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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37A SER 5.7 0.8 + - - -
39A ASP* 3.1 18.2 + - - +
54A LYS* 3.2 43.2 + - - -
55A ILE* 1.3 72.5 - - - +
57A ARG* 1.3 81.4 + - - +
63A LEU* 3.7 1.6 - - - -
64A HIS* 2.6 70.8 + + + +
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Residues in contact with ARG 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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38A ALA 4.9 3.6 - - - +
39A ASP* 3.1 17.3 + - - +
56A TRP* 1.3 90.0 + - - +
58A ARG* 1.3 64.6 + - - +
59A ALA* 3.1 20.8 + - - +
60A GLY 4.0 15.1 - - - +
61A GLY* 4.3 8.7 - - - +
62A ARG 3.0 17.5 - - - +
63A LEU* 3.6 28.7 - - + +
64A HIS* 4.5 2.2 + - - -
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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