Contacts of the strand formed by residues 2 - 11 (chain A) in PDB entry 1DBF
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 MET 2 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 1.3 79.7 - - - +
3A ILE* 1.4 94.0 + - - +
4A ARG* 3.5 40.4 - - - +
96A GLN* 3.4 5.9 - - - +
97A THR 2.8 34.1 + - - +
3C ILE* 4.3 7.0 - - - -
40C GLU 4.0 2.9 - - - +
41C ASP* 3.6 28.7 - - - +
43C VAL* 3.7 10.1 - - + +
96C GLN* 3.6 37.7 - - + +
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Residues in contact with ILE 3 (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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2A MET* 1.4 98.5 - - - +
4A ARG* 1.3 64.7 + - - +
43A VAL* 4.0 9.6 - - + -
94A THR* 3.4 29.6 - - + -
95A VAL 3.2 6.3 - - - +
96A GLN* 3.9 25.1 - - + +
1B MET 4.9 8.5 - - - +
2B MET* 4.3 6.5 - - - -
3B ILE* 4.1 22.9 - - + -
3C ILE* 4.0 23.1 - - + -
43C VAL* 3.3 31.7 - - + +
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Residues in contact with ARG 4 (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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2A MET* 3.5 32.2 - - + +
3A ILE* 1.3 75.7 - - - +
5A GLY* 1.3 67.7 + - - +
93A MET 3.6 0.2 - - - +
94A THR* 3.6 1.0 - - - -
95A VAL* 2.8 35.7 + - + +
97A THR* 3.5 28.7 - - + +
99A VAL 4.0 13.2 + - - +
100A PRO* 5.4 1.6 - - - +
101A GLN* 3.6 46.4 + - - +
104A ILE* 4.3 11.0 - - + -
40C GLU* 2.8 32.7 + - - +
42C VAL 3.8 10.3 + - - -
43C VAL* 3.9 9.9 - - - -
96C GLN* 6.0 0.2 - - - +
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Residues in contact with GLY 5 (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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4A ARG* 1.3 76.1 - - - +
6A ILE* 1.3 63.5 + - - +
92A MET* 4.1 3.8 - - - -
93A MET 3.5 5.4 - - - -
104A ILE* 3.9 6.8 - - - +
106A HIS* 3.5 8.5 + - - -
43C VAL* 2.9 17.6 + - - +
44C GLN* 4.0 15.3 - - - -
72C PRO* 3.3 27.4 - - - +
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Residues in contact with ILE 6 (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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4A ARG 4.4 0.2 - - - +
5A GLY* 1.3 75.7 - - - -
7A ARG* 1.3 69.7 + - - +
31A ILE* 4.0 17.8 - - + +
35A ASN* 3.8 28.3 - - + +
37A THR* 3.9 15.7 - - - +
91A VAL* 3.7 2.8 - - - +
92A MET* 3.5 3.8 - - - -
93A MET* 2.7 51.5 + - + +
95A VAL* 4.0 28.0 - - + -
104A ILE* 3.7 18.4 - - + -
105A ARG 3.6 23.6 - - - +
106A HIS* 3.8 3.1 - - + -
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Residues in contact with ARG 7 (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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6A ILE* 1.3 79.0 - - - +
8A GLY* 1.4 80.6 + - - +
9A ALA* 4.2 2.8 - - - +
31A ILE* 4.4 1.9 - - - +
90A ARG* 3.8 13.1 - - - +
91A VAL* 2.9 21.3 + - - +
92A MET* 3.6 20.4 - - - -
106A HIS* 2.9 24.4 - - + -
107A VAL 3.0 21.2 + - - -
108A TYR* 4.1 12.0 - - - +
251A GOL 2.7 46.6 + - - -
63C ARG* 3.4 0.4 - - - +
72C PRO* 3.9 22.0 - - + -
73C VAL 2.9 30.0 + - - +
74C THR* 3.8 9.7 + - - -
201C SO4 3.3 5.5 + - - -
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Residues in contact with GLY 8 (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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7A ARG* 1.4 89.6 + - - +
9A ALA* 1.3 59.9 + - - +
27A LEU* 4.0 6.3 - - - -
31A ILE* 4.3 2.0 - - - -
90A ARG* 3.4 0.3 - - - -
91A VAL* 2.9 44.1 + - - +
107A VAL 2.9 13.7 - - - -
108A TYR* 4.5 1.8 - - - -
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Residues in contact with ALA 9 (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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7A ARG* 4.2 1.1 - - - +
8A GLY* 1.3 75.7 - - - +
10A THR* 1.3 64.1 + - - +
27A LEU* 3.7 7.6 - - - +
88A CYS* 4.3 1.6 - - - -
89A ILE 3.1 12.1 - - - +
90A ARG* 3.9 14.6 - - + -
107A VAL 2.9 6.4 + - - +
108A TYR* 3.4 17.0 - - + -
109A LEU 2.9 24.9 + - - -
112A ALA* 3.6 17.4 - - + +
115A LEU* 4.0 9.9 - - + -
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Residues in contact with THR 10 (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 ALA* 1.3 76.9 - - - +
11A THR* 1.3 71.8 + - - +
23A LYS* 3.8 35.2 + - + +
24A THR* 4.7 0.7 - - - +
27A LEU* 4.0 17.5 - - + -
88A CYS* 3.3 7.4 - - - -
89A ILE* 2.9 45.8 + - + +
109A LEU* 3.5 17.7 - - - +
110A GLU* 3.2 23.2 - - - +
112A ALA* 3.7 1.8 - - - -
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Residues in contact with THR 11 (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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10A THR* 1.3 84.7 + - - +
12A VAL* 1.3 68.7 + - - +
13A GLU* 5.2 1.6 + - - -
23A LYS* 3.6 12.9 - - - +
85A LEU* 3.5 31.9 - - + -
86A LYS 3.8 10.1 - - - +
87A LYS 3.0 15.0 - - - +
88A CYS* 4.1 1.1 - - - -
89A ILE* 4.7 0.7 - - - +
110A GLU* 3.4 20.5 - - - +
111A LYS* 3.0 36.0 + - + +
112A ALA 3.8 6.7 - - - +
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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