Contacts of the strand formed by residues 23 - 32 (chain A) in PDB entry 4B0O
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 GLY 23 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A THR* 3.4 11.8 - - - +
20A VAL 3.0 27.3 + - - -
21A PHE 3.0 0.8 - - - -
22A GLY* 1.3 79.6 - - - +
24A THR* 1.3 63.9 + - - -
135A ARG* 3.4 17.7 - - - -
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Residues in contact with THR 24 (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 GLN* 3.9 28.7 - - + +
18A LEU 3.2 10.9 + - - +
19A THR* 5.2 2.4 + - - -
20A VAL 4.6 0.2 - - - +
23A GLY* 1.3 75.6 + - - -
25A VAL* 1.3 77.3 + - - +
100A PRO* 4.6 0.3 - - - +
101A ALA* 3.2 46.7 + - + +
135A ARG* 4.4 6.3 - - - +
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Residues in contact with VAL 25 (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 GLN* 3.7 2.1 - - - -
18A LEU* 2.8 37.5 + - + +
20A VAL* 3.7 16.4 - - + -
24A THR* 1.3 81.5 - - - +
26A THR* 1.3 73.8 + - - +
98A TRP* 4.1 18.4 - - + -
99A ILE 3.5 14.1 - - - +
100A PRO* 5.1 0.9 - - + -
101A ALA 4.5 0.4 - - - +
131A LYS* 3.5 23.8 - - + +
134A ALA* 3.9 16.2 - - + -
135A ARG* 3.7 25.1 - - + +
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Residues in contact with THR 26 (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 ILE* 4.0 23.4 - - + +
16A MET 3.6 8.5 - - - +
17A GLN* 2.9 25.5 + - - +
25A VAL* 1.3 73.9 - - - +
27A ALA* 1.3 62.0 + - - +
28A PHE* 3.6 26.8 - - + -
97A VAL 3.8 1.2 - - - +
98A TRP* 3.5 2.9 - - - -
99A ILE* 2.9 56.5 + - + +
100A PRO 4.8 0.5 + - - -
101A ALA* 4.3 10.6 - - - +
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Residues in contact with ALA 27 (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 GLY* 3.3 2.6 - - - -
16A MET* 2.9 44.8 + - + +
18A LEU* 3.7 27.6 - - + -
25A VAL 3.9 0.2 + - - -
26A THR* 1.3 74.8 - - - +
28A PHE* 1.3 62.3 + - - +
29A LEU* 3.9 13.2 - - + -
58A ALA 3.7 1.6 - - - +
97A VAL 3.5 3.6 - - - -
98A TRP* 3.7 18.4 - - + +
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Residues in contact with PHE 28 (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 ILE* 3.9 12.3 - - + -
6A ILE* 3.6 25.4 - - + -
13A VAL* 3.9 24.7 - - + -
14A ARG 3.9 4.9 - - - -
15A GLY* 3.3 27.8 - - - -
26A THR* 3.6 29.2 - - + -
27A ALA* 1.3 72.1 - - - +
29A LEU* 1.3 62.3 + - - +
30A GLY 4.0 0.2 + - - -
31A ILE* 3.7 19.9 - - + +
58A ALA* 3.4 9.2 - - + -
95A LEU 4.1 1.2 - - - +
96A ASN* 3.2 5.2 - - - +
97A VAL* 2.8 49.5 + - + +
99A ILE* 4.4 13.0 - - + -
185A PHE* 3.8 22.2 - + - -
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Residues in contact with LEU 29 (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 MET* 4.3 17.3 - - + -
27A ALA* 4.2 13.5 - - + -
28A PHE* 1.3 78.4 - - - +
30A GLY* 1.3 61.5 + - - +
31A ILE 3.7 0.2 - - - -
57A ASN 4.6 0.3 - - - +
58A ALA* 2.8 31.2 + - - +
60A LYS* 3.0 35.3 - - - +
61A TYR* 3.8 31.4 - - + +
96A ASN* 3.6 8.5 - - + +
98A TRP* 3.9 33.9 - - + +
1296A GLY* 4.2 20.6 - - - +
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Residues in contact with GLY 30 (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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29A LEU* 1.3 74.4 - - - +
31A ILE* 1.3 63.0 + - - +
32A PRO* 3.8 0.3 - - - +
56A TRP* 2.9 26.8 + - - -
57A ASN 4.8 0.2 - - - +
58A ALA* 4.5 0.4 - - - -
60A LYS 3.8 4.4 + - - -
62A ALA* 4.0 25.4 - - - +
94A TYR* 3.8 10.0 - - - -
95A LEU 3.2 4.3 + - - -
96A ASN* 3.1 15.7 + - - -
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Residues in contact with ILE 31 (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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8A THR* 5.7 0.4 - - + -
13A VAL* 4.4 20.9 - - + -
28A PHE* 3.7 24.7 - - + +
30A GLY* 1.3 72.3 - - - -
32A PRO* 1.3 81.4 - - + +
33A TYR 3.6 0.2 + - - -
52A TRP* 4.9 4.3 - - + -
56A TRP* 4.4 1.8 - - - +
58A ALA* 3.9 18.8 - - + -
94A TYR* 3.2 1.5 - - - -
95A LEU* 2.7 54.2 + - + +
97A VAL* 4.1 6.7 - - + -
177A TRP* 3.9 39.5 - - + +
185A PHE* 4.3 8.7 - - + -
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Residues in contact with PRO 32 (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 ASN* 5.9 0.3 + - - -
30A GLY 3.8 0.2 - - - +
31A ILE* 1.3 98.3 - - + +
33A TYR* 1.3 59.1 + - - +
34A ALA 4.7 4.0 - - - +
49A LEU* 3.4 24.4 - - + +
52A TRP* 4.1 14.7 - - + -
56A TRP* 3.5 48.7 - - + +
93A LEU 3.6 3.6 - - - +
94A TYR* 3.5 24.6 - - + -
177A TRP* 4.3 6.1 + - - -
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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