Contacts of the strand formed by residues 119 - 125 (chain A) in PDB entry 3A61
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 ILE 119 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94A LEU* 4.7 11.7 - - + -
107A GLN* 3.9 32.5 - - + +
108A VAL 3.4 13.0 - - - +
109A ARG* 4.2 20.6 - - + +
117A GLY 4.2 7.0 - - - +
118A LYS* 1.3 85.1 - - - +
120A PHE* 1.3 80.3 + - - +
174A TYR* 4.1 23.6 + - + +
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Residues in contact with PHE 120 (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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91A PHE* 4.6 13.5 - + - -
107A GLN* 3.2 10.4 - - - +
108A VAL* 2.8 44.1 + - + +
110A LYS* 4.7 15.7 - - + -
115A ASN* 4.7 9.4 - - + -
118A LYS* 3.7 50.3 - - + -
119A ILE* 1.3 85.5 - - - +
121A ALA* 1.3 59.5 + - - +
159A ILE* 3.9 31.4 - - + -
160A TYR* 4.9 5.6 - + - -
171A ILE* 4.1 16.4 - - + -
172A LEU 3.7 15.9 - - - +
173A GLU* 4.5 5.4 - - - -
174A TYR* 3.8 11.6 - - - +
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Residues in contact with ALA 121 (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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97A LEU* 4.3 10.3 - - + -
105A VAL* 4.7 3.1 - - + -
106A PHE 3.3 7.0 - - - +
120A PHE* 1.3 76.3 - - - +
122A MET* 1.3 61.3 + - - +
123A LYS 4.0 1.4 + - - -
170A LEU 3.6 0.2 - - - +
171A ILE* 3.2 3.2 - - - -
172A LEU* 2.6 45.1 + - + +
173A GLU 4.3 0.9 - - - +
174A TYR* 4.2 2.0 - - + +
400A STU 3.6 41.3 - - + +
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Residues in contact with MET 122 (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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88A PRO* 5.0 10.3 - - + +
91A PHE* 4.1 17.5 - - - -
93A LEU* 4.3 22.4 - - + -
105A VAL* 3.7 2.3 - - - +
106A PHE* 2.7 40.7 + - + +
108A VAL* 4.0 16.2 - - + -
121A ALA* 1.3 73.4 - - - +
123A LYS* 1.3 57.9 + - - +
124A VAL* 3.5 33.4 + - + +
162A PHE* 5.4 0.4 - - - -
169A TYR* 3.8 22.4 - - + -
170A LEU 2.9 6.5 - - - +
171A ILE* 3.1 30.1 - - + -
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Residues in contact with LYS 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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100A GLY 5.3 4.5 + - - -
101A GLY* 5.8 1.4 - - - -
102A TYR* 3.7 28.5 + - - +
104A LYS 3.6 10.1 - - - +
105A VAL* 3.9 15.0 - - + +
121A ALA 4.0 1.6 - - - -
122A MET* 1.3 72.3 - - - +
124A VAL* 1.3 61.7 + - - +
125A LEU* 3.8 19.9 - - + +
143A GLU* 3.5 36.7 + - - +
168A LEU 3.4 1.6 - - - +
169A TYR* 3.3 2.9 - - - -
170A LEU* 2.7 51.8 + - + +
172A LEU* 4.5 12.0 - - + +
236A ASP* 4.5 5.9 + - - -
237A PHE 4.6 2.0 + - - -
400A STU 4.1 29.2 - - + -
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Residues in contact with VAL 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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102A TYR 4.5 0.2 - - - +
103A GLY* 3.4 5.7 - - - -
104A LYS* 2.8 33.7 + - + +
106A PHE* 4.3 16.2 - - + -
122A MET* 3.5 25.4 - - + +
123A LYS* 1.3 76.0 - - - +
125A LEU* 1.3 63.3 + - - +
126A LYS* 4.1 1.8 + - + +
167A LYS* 4.4 21.5 - - + -
168A LEU 3.3 2.9 - - - +
169A TYR* 3.2 41.5 - - + -
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Residues in contact with LEU 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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102A TYR* 2.7 48.9 - - + +
103A GLY* 3.9 1.8 - - - +
123A LYS* 3.8 28.7 + - + +
124A VAL* 1.3 72.0 - - - +
126A LYS* 1.3 66.1 + - - +
143A GLU* 4.3 15.5 - - + +
166A GLY 3.5 3.1 - - - +
167A LYS* 4.5 1.3 - - - -
168A LEU* 2.7 62.0 + - + +
170A LEU* 5.2 0.4 - - + -
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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