Contacts of the strand formed by residues 31 - 37 (chain A) in PDB entry 1SBB
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 ASN 31 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A HIS* 3.5 1.9 - - - +
30A ASN* 1.3 87.5 - - - +
32A MET* 1.3 68.5 + - - +
33A TYR* 3.2 32.2 + - + +
48A TYR* 4.8 2.2 - - - -
49A SER 3.0 16.6 + - - +
50A TYR* 3.5 28.8 - - - +
94A SER* 3.3 2.1 - - - -
95A GLY 3.1 36.3 + - - +
96A GLY 4.1 5.6 + - - -
97A GLY* 4.5 5.8 - - - -
98A ARG 4.9 1.4 - - - +
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Residues in contact with MET 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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23A CYS* 3.5 40.2 - - - +
25A GLN* 3.4 42.6 - - + +
30A ASN 4.0 0.6 + - - -
31A ASN* 1.3 80.7 - - - +
33A TYR* 1.3 65.4 + - - +
48A TYR* 3.4 2.9 - - - +
49A SER 2.9 29.2 + - - +
69A ARG* 3.5 28.3 - - - +
72A GLN 3.8 4.0 - - - +
73A GLU 4.1 0.9 - - - +
74A GLN 4.2 4.5 - - - -
75A PHE* 3.7 32.5 - - + -
92A CYS* 4.0 2.9 - - - -
93A ALA 3.3 6.1 - - - +
94A SER* 4.0 3.8 - - - -
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Residues in contact with TYR 33 (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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31A ASN* 3.2 33.5 + - + -
32A MET* 1.3 77.1 - - - +
34A TRP* 1.3 63.1 + - - +
35A TYR* 3.7 27.4 - - + -
45A LEU* 3.7 15.3 - - + -
47A HIS 3.9 4.5 - - - -
48A TYR* 3.5 30.3 - + + -
75A PHE* 3.9 3.6 - - - -
91A PHE 4.5 0.2 - - - -
92A CYS* 3.3 13.2 - - - -
93A ALA* 2.9 35.5 + - + +
95A GLY 4.6 3.1 - - - -
96A GLY 2.5 30.2 + - - -
97A GLY 3.0 15.0 - - - -
98A ARG* 3.8 20.2 - - + -
106A GLN* 4.2 16.8 - - + -
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Residues in contact with TRP 34 (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 GLN* 3.8 19.7 - - + -
21A LEU* 3.8 30.7 - - + -
22A SER 4.0 4.9 - - - -
23A CYS* 3.9 22.2 - - + +
33A TYR* 1.3 74.6 - - - +
35A TYR* 1.3 64.3 + - - +
45A LEU* 3.5 4.2 - - - +
46A ILE* 2.8 28.3 + - + +
47A HIS 3.1 14.5 + - - +
75A PHE* 2.9 51.0 + + + -
76A SER 4.2 4.3 - - - -
77A LEU* 3.9 48.3 - - + +
90A TYR* 3.3 37.0 - - + -
91A PHE 3.5 15.9 - - - -
92A CYS* 4.0 5.8 - - + -
112A THR* 4.8 1.3 - - - -
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Residues in contact with TYR 35 (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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33A TYR* 3.7 19.7 - - + -
34A TRP* 1.3 75.7 - - - +
36A ARG* 1.3 62.7 + - - +
43A LEU* 3.6 28.3 - - + -
44A ARG 3.1 10.1 - - - +
45A LEU* 3.6 40.8 - - + +
46A ILE* 4.2 3.6 - - - -
90A TYR* 3.3 13.2 - - - +
91A PHE* 2.8 39.5 + - + +
93A ALA* 4.1 4.0 - - + -
98A ARG* 6.0 0.2 - - - +
99A GLY 5.3 1.4 + - - -
101A TYR* 3.6 22.4 - + - -
106A GLN* 2.5 35.2 + - - -
108A PHE* 3.4 31.2 - + - -
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Residues in contact with ARG 36 (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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35A TYR* 1.3 77.6 - - - +
37A GLN* 1.3 59.2 + - - +
38A ASP* 3.2 27.3 + - - +
42A GLY 3.6 3.3 - - - +
43A LEU* 4.6 2.5 - - - -
44A ARG* 3.0 33.6 + - + +
46A ILE* 4.0 6.3 - - + -
60A ILE* 3.3 35.4 - - + +
65A TYR* 2.8 36.0 + - - -
85A SER 3.0 28.7 + - - -
86A GLN* 3.9 2.9 - - - +
87A THR 3.1 22.2 + - - -
88A SER* 3.4 12.2 - - - +
89A VAL 3.4 5.4 - - - -
90A TYR* 3.8 14.4 - - + -
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Residues in contact with GLN 37 (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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36A ARG* 1.3 70.5 - - - +
38A ASP* 1.3 73.3 + - - +
39A THR* 5.3 0.8 - - - +
41A HIS 3.7 8.5 + - - -
42A GLY* 3.0 25.0 + - - -
43A LEU* 3.7 8.3 - - + +
88A SER* 2.6 20.6 + - - -
89A VAL* 2.9 21.2 + - + +
91A PHE* 3.6 29.3 - - + -
59C ASP* 4.7 4.6 + - - -
99C GLY* 5.0 9.9 - - - +
101C TYR* 2.4 40.3 + - + -
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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