Contacts of the strand formed by residues 48 - 55 (chain A) in PDB entry 1R88
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 48 (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 28.8 + - - +
46A MET* 3.9 16.5 + - + +
47A GLY* 1.3 80.7 - - - +
49A ASP* 1.3 75.0 + - - +
50A ILE* 3.8 25.7 - - + +
51A PRO* 5.9 1.6 - - - +
99A GLY* 3.9 22.8 + - - -
113A SER* 3.0 40.8 + - - -
116A TRP* 4.0 6.5 - - - +
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Residues in contact with ASP 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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40A MET* 3.8 42.8 - - + +
41A VAL 3.5 5.4 - - - +
42A PRO* 3.3 26.8 - - - +
48A ARG* 1.3 88.1 + - - +
50A ILE* 1.3 61.0 + - - +
51A PRO* 3.8 7.1 - - - +
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Residues in contact with ILE 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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40A MET* 3.6 2.2 - - - -
41A VAL 2.9 30.1 + - - +
43A SER* 3.8 16.2 - - - -
46A MET* 3.9 15.7 - - + -
48A ARG* 3.8 43.3 - - + +
49A ASP* 1.3 74.3 - - - +
51A PRO* 1.3 71.9 - - + +
52A VAL* 3.4 6.6 + - + +
97A PRO* 4.3 1.6 - - + -
98A ALA 3.5 22.4 - - - +
116A TRP* 3.8 8.1 - - + -
119A PHE* 3.6 40.4 - - + -
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Residues in contact with PRO 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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39A LEU 3.4 8.3 - - - +
40A MET* 3.9 19.3 - - + -
48A ARG* 5.9 1.8 - - - +
49A ASP 3.8 7.6 - - - +
50A ILE* 1.3 87.9 - - + +
52A VAL* 1.3 62.7 - - - +
53A ALA 4.2 0.7 - - - -
72A PRO 4.2 12.1 - - - +
73A ASP* 3.5 31.0 - - + +
97A PRO* 3.5 0.2 - - - +
98A ALA* 2.8 38.0 + - + +
99A GLY* 5.6 0.9 - - - -
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Residues in contact with VAL 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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37A GLU 3.4 0.9 - - - +
38A ASN* 4.9 1.3 - - - -
39A LEU* 3.0 44.1 + - + +
41A VAL* 3.8 22.9 - - + -
50A ILE* 3.6 15.7 - - + +
51A PRO* 1.3 78.2 - - - +
53A ALA* 1.3 69.3 + - - +
54A PHE* 3.4 1.6 + - + -
95A VAL* 3.6 30.5 - - + -
96A ALA 3.7 8.7 - - - +
97A PRO* 4.2 13.7 - - + -
119A PHE* 4.3 1.8 - - + -
124A LEU* 4.2 14.1 - - + -
128A LEU* 5.8 0.7 - - + -
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Residues in contact with ALA 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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36A TYR* 3.4 27.4 - - + +
37A GLU 3.5 6.7 - - - -
38A ASN* 4.9 1.6 - - - +
51A PRO 4.2 0.2 - - - -
52A VAL* 1.3 71.7 - - - +
54A PHE* 1.3 57.7 + - - +
74A VAL* 5.7 3.1 - - + -
75A SER 5.9 0.7 - - - +
78A VAL* 3.9 22.9 - - + -
84A MET* 4.0 7.0 - - + +
94A VAL 3.5 1.4 - - - +
95A VAL* 3.4 4.9 - - - -
96A ALA* 2.9 39.8 + - + +
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Residues in contact with PHE 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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36A TYR* 3.6 4.8 - - - +
37A GLU* 2.9 61.4 + - + +
39A LEU* 3.5 33.0 - - + -
52A VAL* 4.9 2.0 - - + -
53A ALA* 1.3 74.3 - - - +
55A LEU* 1.3 60.2 + - - +
56A ALA* 3.7 30.1 + - + -
93A SER* 3.9 25.4 - - - -
94A VAL 3.3 11.4 - - - -
95A VAL* 3.9 10.1 - - + -
128A LEU* 4.3 5.6 - - + -
132A ARG* 3.8 29.6 - - + -
134A LEU* 4.1 18.4 - - + -
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Residues in contact with LEU 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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34A ALA* 5.8 6.3 - - + -
35A PRO 3.5 24.9 - - - +
36A TYR* 4.3 4.0 - - + -
54A PHE* 1.3 74.5 - - - +
56A ALA* 1.3 76.3 + - - +
84A MET* 3.7 35.9 - - + +
88A ALA* 3.9 33.7 - - + -
89A GLY 5.4 0.4 - - - +
92A ILE 4.5 1.2 - - - +
93A SER* 3.3 3.8 - - - -
94A VAL* 2.9 37.7 + - + +
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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