Contacts of the strand formed by residues 104 - 112 (chain A) in PDB entry 1BMZ
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A CYS 3.7 25.7 - - - +
11A PRO* 3.5 11.8 - - - +
61A GLU* 3.0 46.0 + - - +
102A PRO* 3.6 23.2 + - - +
103A ARG* 1.3 85.2 + - - +
105A TYR* 1.3 59.3 + - - +
106A THR* 4.2 1.6 - - - +
121A VAL 3.6 1.7 - - - +
122A VAL* 3.4 6.1 - - - +
123A THR* 2.6 53.0 + - - +
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Residues in contact with TYR 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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11A PRO 2.8 12.7 + - - +
12A LEU* 3.3 15.5 - - + +
13A MET* 2.8 27.2 + - - +
64A PHE* 3.5 24.9 - + - -
95A PHE* 3.9 12.1 - + - -
96A THR 4.4 2.4 + - - -
97A ALA* 3.5 9.8 - - + -
98A ASN* 2.9 45.3 + - - -
99A ASP* 4.9 2.3 + - - -
103A ARG* 3.8 26.7 - - + +
104A ARG* 1.3 73.3 - - - +
106A THR* 1.3 61.5 + - - +
107A ILE* 4.0 6.7 - - + -
120A ALA* 5.7 0.2 - - + -
121A VAL 3.7 2.2 - - - -
122A VAL* 3.7 20.8 - - + +
87B PHE* 3.7 31.9 - + - -
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Residues in contact with THR 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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13A MET* 3.3 38.7 - - + +
15A LYS* 4.9 7.2 - - + -
104A ARG* 5.4 1.4 - - - +
105A TYR* 1.3 73.6 + - - +
107A ILE* 1.3 69.0 + - - +
108A ALA* 3.9 6.0 + - + +
119A THR 3.8 0.7 - - - +
120A ALA* 3.4 4.2 - - - -
121A VAL* 2.9 51.8 + - + +
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Residues in contact with ILE 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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12A LEU* 4.2 19.3 - - + -
13A MET 2.8 9.6 + - - +
14A VAL* 3.3 16.3 - - + +
15A LYS* 2.9 25.1 + - - +
71A VAL* 4.5 10.1 - - + -
73A ILE* 5.2 4.3 - - + -
93A VAL* 4.0 18.8 - - + -
95A PHE* 4.1 17.3 - - + -
105A TYR* 4.6 6.5 - - + -
106A THR* 1.3 78.1 - - - +
108A ALA* 1.3 63.4 + - - +
118A THR* 3.7 19.7 - - - +
119A THR 3.6 3.6 - - - +
120A ALA* 4.2 3.8 - - + -
87B PHE* 3.6 35.7 - - + -
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Residues in contact with ALA 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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15A LYS* 3.2 18.4 - - + +
106A THR* 3.9 7.3 - - + +
107A ILE* 1.3 75.7 - - - +
109A ALA* 1.3 61.6 + - - +
118A THR* 3.1 7.7 + - - -
119A THR* 2.8 46.6 + - + +
121A VAL* 6.0 3.4 - - + -
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Residues in contact with ALA 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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14A VAL* 6.0 0.2 - - + -
15A LYS 2.8 11.3 + - - +
16A VAL* 3.4 5.8 - - + +
17A LEU* 2.9 28.2 + - - +
73A ILE* 3.7 29.8 - - + -
91A ALA* 5.8 2.2 - - + -
108A ALA* 1.3 76.1 - - - +
110A LEU* 1.3 59.6 + - - +
111A LEU* 4.0 15.9 - - + -
116A TYR* 5.9 1.3 - - + -
117A SER 3.3 7.6 - - - +
118A THR* 4.7 5.8 - - - +
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Residues in contact with LEU 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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17A LEU* 3.7 29.6 - - + +
18A ASP 4.5 0.2 - - - -
19A ALA* 3.8 31.6 - - + +
109A ALA* 1.3 74.9 - - - +
111A LEU* 1.3 60.9 + - - +
116A TYR* 3.3 6.9 - - - +
117A SER* 2.9 45.5 + - - +
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Residues in contact with LEU 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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16A VAL* 3.6 27.8 - - + -
17A LEU 2.8 14.1 + - - +
18A ASP* 3.9 1.2 - - - -
19A ALA* 2.9 28.4 + - - +
25A ALA* 4.5 3.8 - - + -
28A VAL* 5.1 1.8 - - + -
73A ILE* 5.0 2.7 - - + -
75A THR* 3.7 37.7 - - + -
78A TYR* 4.2 24.0 - - + -
79A TRP* 3.3 20.0 - - + +
91A ALA* 5.0 1.8 - - + -
109A ALA* 4.2 17.5 - - + -
110A LEU* 1.3 79.3 - - - +
112A SER* 1.3 62.1 + - - +
115A SER 4.1 1.1 - - - -
116A TYR* 4.0 16.4 - - + -
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Residues in contact with SER 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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19A ALA* 3.3 25.5 - - - +
20A VAL* 4.4 2.0 - - - +
79A TRP* 3.4 14.1 + - - -
88A HIS* 5.2 1.7 + - - -
110A LEU 4.3 0.2 + - - -
111A LEU* 1.3 70.9 - - - +
113A PRO* 1.3 77.5 - - - +
114A TYR 3.3 1.3 - - - -
115A SER* 2.9 36.9 + - - +
116A TYR* 5.3 0.3 - - - +
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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