Contacts of the strand formed by residues 103 - 112 (chain A) in PDB entry 2R9A
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 ALA 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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45A TRP* 3.7 2.1 + - - -
99A CYS* 3.5 9.5 - - - +
100A VAL* 2.7 49.8 + - + +
101A ALA 3.2 0.7 - - - +
102A ASP* 1.3 75.0 - - - +
104A LEU* 1.3 61.8 + - - +
105A ILE* 5.5 1.6 - - + -
123A CYS 3.3 15.3 - - - +
124A MSE 4.6 5.4 - - + +
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Residues in contact with LEU 104 (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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23A LEU* 3.7 9.0 - - + -
38A VAL* 3.5 31.2 - - + -
45A TRP* 3.6 34.0 - - + +
97A CYS* 3.4 30.7 - - - -
98A ASP 3.3 11.0 - - - +
99A CYS* 3.2 29.2 - - - -
103A ALA* 1.3 74.7 - - - +
105A ILE* 1.3 67.5 + - - +
106A LEU* 4.1 3.6 - - + +
121A PHE 3.6 0.7 - - - +
123A CYS* 2.7 42.2 + - + +
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Residues in contact with ILE 105 (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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96A SER 3.8 0.7 - - - +
97A CYS* 3.6 4.5 - - - -
98A ASP* 2.8 43.6 + - + +
100A VAL* 3.7 32.5 - - + -
103A ALA* 5.4 1.8 - - + -
104A LEU* 1.3 80.1 - - - +
106A LEU* 1.3 61.2 + - - +
107A ARG* 3.9 42.7 + - + +
120A ASN* 4.0 15.3 - - + -
121A PHE 3.2 8.5 - - - +
122A HIS* 3.8 28.9 - - + +
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Residues in contact with LEU 106 (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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16A LEU* 4.9 12.3 - - + -
18A LEU* 4.0 20.4 - - + -
23A LEU* 4.0 26.0 - - + -
36A LEU* 4.9 10.8 - - + -
38A VAL* 5.3 8.3 - - + -
80A LEU* 5.8 2.7 - - + -
95A PHE* 4.5 18.8 - - + -
96A SER 3.7 10.3 - - - +
97A CYS* 4.3 5.8 - - - -
104A LEU* 4.1 4.4 - - + -
105A ILE* 1.3 72.2 - - - +
107A ARG* 1.3 59.8 + - - +
120A ASN* 3.3 0.9 - - - -
121A PHE* 2.4 76.9 + - + +
123A CYS* 5.3 6.0 - - - -
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Residues in contact with ARG 107 (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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95A PHE* 3.3 14.6 - - - +
96A SER* 3.0 49.7 + - - +
98A ASP* 2.5 28.6 + - - +
105A ILE* 3.9 33.2 - - + +
106A LEU* 1.3 75.4 - - - +
108A VAL* 1.3 63.1 + - - +
109A ARG* 6.1 2.0 - - + -
119A TRP 3.5 4.3 - - - -
120A ASN* 3.1 39.7 + - - +
122A HIS* 6.0 0.6 - - - -
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Residues in contact with VAL 108 (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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76A LEU* 4.6 5.6 - - + -
79A LEU* 3.6 28.9 - - + -
80A LEU* 6.1 0.4 - - + -
93A ALA* 5.4 0.4 - - + -
94A THR 3.8 3.4 - - - +
95A PHE* 3.9 20.9 - - + -
107A ARG* 1.3 77.7 - - - +
109A ARG* 1.3 72.3 + - - +
110A SER* 3.8 12.6 - - - +
117A PHE* 4.4 2.9 - - + +
118A TYR* 3.5 6.9 - - - +
119A TRP* 2.7 44.5 + - + +
120A ASN* 5.1 0.7 - - - +
121A PHE* 3.6 31.4 - - + -
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Residues in contact with ARG 109 (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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93A ALA* 3.4 2.4 - - - -
94A THR* 2.9 64.3 + - + +
107A ARG* 5.8 2.9 - - + -
108A VAL* 1.3 79.1 - - - +
110A SER* 1.3 63.6 + - - +
116A PRO* 5.1 8.3 - - - +
117A PHE 3.7 3.4 - - - -
118A TYR* 3.1 41.1 + - + -
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Residues in contact with SER 110 (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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75A HIS* 3.3 20.7 + - - -
79A LEU* 3.6 11.8 - - - +
93A ALA* 3.3 25.4 - - - +
108A VAL* 3.8 7.6 - - - +
109A ARG* 1.3 81.0 + - - +
111A GLU* 1.3 57.7 + - - +
116A PRO* 3.2 6.4 - - - +
117A PHE* 2.3 46.4 + - - -
118A TYR* 5.7 0.4 - - - -
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Residues in contact with GLU 111 (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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75A HIS* 2.6 28.4 + - - -
110A SER* 1.3 80.6 - - - +
112A LEU* 1.3 53.8 + - - +
113A SER 5.7 0.2 - - - +
114A GLY* 4.2 18.4 - - - +
115A LEU 3.2 16.4 - - - +
116A PRO* 4.3 2.7 - - + -
117A PHE* 4.4 0.9 - - - -
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Residues in contact with LEU 112 (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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65A LEU* 5.0 17.7 - - + +
67A ALA* 5.8 4.5 - - + -
71A ALA* 3.8 24.7 - - + +
72A PHE* 5.2 11.2 - - + -
75A HIS* 3.6 38.4 - - + -
111A GLU* 1.3 72.1 - - - +
113A SER* 1.3 84.9 + - - +
114A GLY 3.2 1.1 - - - -
115A LEU* 2.6 26.4 + - - +
117A PHE* 4.1 14.4 - - + +
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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