Contacts of the strand formed by residues 122 - 128 (chain A) in PDB entry 1RJF
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 LEU 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A LEU* 3.9 28.0 - - + -
97A GLU 5.1 1.1 - - - +
99A VAL* 3.5 15.0 - - + +
101A VAL* 3.8 21.3 - - + -
115A LEU* 3.3 42.4 - - + +
116A LEU* 3.1 24.7 - - + +
119A PHE* 3.3 22.4 + - + +
120A PRO 3.3 1.0 - - - -
121A HIS* 1.3 76.3 - - - +
123A ALA* 1.3 80.0 + - - +
124A TYR* 4.8 6.7 - - + -
168A ARG* 3.1 12.7 + - - +
338A GOL 4.2 2.7 - - - -
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Residues in contact with ALA 123 (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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99A VAL 3.1 7.8 + - - +
100A GLN* 4.1 19.3 - - + +
101A VAL* 3.2 12.0 + - - +
121A HIS 3.9 1.6 + - - -
122A LEU* 1.3 93.7 - - - +
124A TYR* 1.3 62.9 + - - +
125A VAL* 5.7 3.1 - - + -
168A ARG* 3.6 14.1 - - + +
189A CYS 5.8 3.6 - - - +
338A GOL 4.0 13.4 + - - +
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Residues in contact with TYR 124 (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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101A VAL* 3.5 39.9 - - + +
103A ASN* 2.8 35.8 + - + +
111A ARG* 3.5 15.3 - - - +
112A MET* 3.6 35.8 - - + -
115A LEU* 4.4 13.0 - - + -
116A LEU* 4.1 11.2 - - + -
122A LEU* 4.8 9.9 - - + -
123A ALA* 1.3 75.9 - - - +
125A VAL* 1.3 81.1 + - - +
126A ASP* 3.5 26.7 - - - -
168A ARG 3.1 12.3 + - - +
169A TYR* 3.6 13.3 + + + -
170A LYS* 3.1 24.0 + - - +
199A ILE* 4.1 0.4 - - + +
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Residues in contact with VAL 125 (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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100A GLN* 5.9 1.6 - - + -
101A VAL 3.0 17.1 + - - +
102A VAL* 3.6 7.4 - - + -
103A ASN 3.1 21.3 + - - -
123A ALA* 5.4 3.6 - - + -
124A TYR* 1.3 89.3 - - - +
126A ASP* 1.3 61.6 + - - +
127A ILE* 3.6 24.0 + - + +
162A PHE* 5.4 0.7 - - + -
170A LYS* 3.3 19.3 - - + +
172A ALA* 5.3 5.4 - - + -
189A CYS* 3.8 44.6 - - + +
190A THR* 4.4 7.6 - - + -
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Residues in contact with ASP 126 (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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103A ASN* 3.7 5.6 + - - +
106A CYS* 3.1 20.2 - - - +
109A ASP* 4.8 0.9 - - - +
112A MET* 3.3 14.4 - - - +
124A TYR* 3.5 18.0 - - - -
125A VAL* 1.3 71.9 - - - +
127A ILE* 1.3 63.8 + - - +
136A LYS* 3.0 23.0 + - - -
169A TYR* 2.7 26.5 + - - +
170A LYS 2.9 8.6 + - - +
171A LEU* 3.5 22.0 - - + -
172A ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 127 (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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102A VAL* 3.7 28.0 - - + -
103A ASN 3.3 9.7 + - - +
104A LEU* 4.3 10.3 - - + -
105A GLY 3.0 26.2 + - - -
106A CYS* 3.3 6.0 + - - -
125A VAL* 3.7 18.8 - - + +
126A ASP* 1.3 80.3 - - - +
128A ASP* 1.3 66.1 + - - +
172A ALA* 3.6 5.2 - - + +
174A CYS* 3.6 29.6 - - + -
176A LEU* 3.9 20.0 - - + -
182A THR* 6.0 2.2 - - + +
185A LEU* 3.9 20.6 - - + -
186A LEU* 4.4 11.2 - - + -
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Residues in contact with ASP 128 (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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9A ASP* 5.3 1.2 - - - +
105A GLY* 3.5 15.4 - - - +
106A CYS* 4.0 9.9 - - - -
107A GLY* 3.3 25.0 + - - +
127A ILE* 1.3 77.6 - - - +
129A TYR* 1.3 80.2 + - - +
132A SER* 3.1 25.0 + - - -
133A VAL* 3.5 22.7 - - + +
172A ALA 3.5 3.6 + - - -
173A ALA* 3.6 0.3 - - - -
174A CYS 3.2 24.0 + - - -
176A LEU* 5.3 5.2 - - - +
203A LEU* 5.2 2.9 - - - +
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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