Contacts of the strand formed by residues 31 - 37 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C HIS* 3.7 1.9 - - - +
30C ASN* 1.3 88.1 - - - +
32C MET* 1.3 65.2 + - - +
33C TYR* 3.2 28.3 + - + +
48C TYR* 4.9 1.2 - - - -
49C SER 3.2 10.2 + - - +
50C TYR* 3.5 35.6 - - - +
94C SER* 3.1 4.9 - - - -
95C GLY 2.9 44.3 + - - +
96C GLY 3.7 4.4 + - - +
97C GLY* 4.6 5.8 - - - -
98C ARG 4.9 0.8 - - - +
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Residues in contact with MET 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C VAL* 5.3 0.2 - - + -
23C CYS* 3.5 33.0 - - + -
25C GLN* 3.5 41.3 - - + +
30C ASN 3.9 0.8 + - - -
31C ASN* 1.3 79.2 - - - +
33C TYR* 1.3 69.7 + - - +
48C TYR* 3.5 1.0 - - - +
49C SER 2.9 29.7 + - - +
69C ARG* 3.5 31.0 - - - +
72C GLN 3.8 3.6 - - - +
73C GLU 4.0 13.2 - - - +
75C PHE* 3.6 28.6 - - + -
92C CYS* 4.0 4.0 - - - -
93C ALA 3.2 7.6 - - - +
94C SER* 3.9 4.7 - - - -
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Residues in contact with TYR 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C ASN* 3.2 31.1 + - + -
32C MET* 1.3 77.2 - - - +
34C TRP* 1.3 62.7 + - - +
35C TYR* 3.5 26.7 - - + -
45C LEU* 3.8 13.0 - - + -
47C HIS 4.0 2.0 - - - -
48C TYR* 3.3 29.2 - + + -
75C PHE* 3.8 6.7 - - - -
91C PHE 4.4 0.4 - - - -
92C CYS* 3.4 13.5 - - - -
93C ALA* 2.9 34.7 + - + -
95C GLY 4.7 2.9 - - - -
96C GLY 2.5 29.8 + - - -
97C GLY 3.0 13.0 - - - -
98C ARG* 3.0 29.0 + - + -
106C GLN* 3.9 19.3 - - + -
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Residues in contact with TRP 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C GLN* 3.9 23.8 - - + -
7C SER 5.7 0.2 - - - -
21C LEU* 3.6 33.7 - - + -
22C SER 3.7 17.7 - - - -
23C CYS* 3.8 11.3 - - + +
33C TYR* 1.3 75.1 - - - +
35C TYR* 1.3 61.9 + - - +
45C LEU* 3.9 1.8 - - - +
46C ILE* 2.9 29.9 + - - +
47C HIS 3.2 15.2 + - - +
67C ALA* 5.5 0.2 - - + -
75C PHE* 3.0 48.3 + + + -
76C SER 4.0 2.2 - - - -
77C LEU* 3.5 46.7 - - + +
90C TYR* 3.7 29.6 - - + -
91C PHE 3.5 22.2 - - - -
92C CYS* 4.1 5.8 - - + -
112C THR* 4.8 1.1 - - - -
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Residues in contact with TYR 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C TYR* 3.5 26.3 - - + -
34C TRP* 1.3 75.6 - - - +
36C ARG* 1.3 62.1 - - - +
43C LEU* 3.6 29.6 - - + -
44C ARG 3.1 8.3 - - - +
45C LEU* 3.7 33.0 - - + -
46C ILE* 4.2 3.6 - - - +
90C TYR* 3.3 12.1 - - - +
91C PHE* 2.8 40.8 + - + +
93C ALA* 3.9 5.2 - - + -
98C ARG* 6.0 0.3 - - - +
99C GLY 5.3 0.9 + - - -
101C TYR* 3.4 28.5 - + - -
106C GLN* 2.5 35.9 + - - -
108C PHE* 3.8 22.9 - + - -
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Residues in contact with ARG 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C TYR* 1.3 76.1 - - - +
37C GLN* 1.3 60.9 + - - +
38C ASP* 2.9 35.1 + - - +
42C GLY 3.6 3.3 - - - +
43C LEU* 4.4 2.9 - - - -
44C ARG* 3.1 33.1 + - + +
46C ILE* 4.0 6.3 - - + -
60C ILE* 3.6 32.4 - - + +
65C TYR* 3.0 29.0 + - - -
85C SER 3.1 28.5 + - - -
86C GLN* 4.0 2.5 - - - +
87C THR 3.2 15.6 + - - -
88C SER* 3.3 12.3 + - - +
89C VAL 3.4 5.4 - - - -
90C TYR* 3.7 13.7 - - + -
91C PHE 4.8 0.2 - - - +
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Residues in contact with GLN 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A ASP* 4.9 5.1 + - - -
98A ARG* 6.2 0.2 - - - +
99A GLY* 5.0 9.4 - - - -
101A TYR* 2.5 38.0 + - + -
36C ARG* 1.3 71.2 - - - +
38C ASP* 1.3 76.3 + - - +
39C THR* 4.8 2.0 - - - +
41C HIS 3.9 2.0 + - - -
42C GLY* 3.5 22.1 + - - +
43C LEU* 3.8 7.4 - - + +
88C SER* 2.8 19.9 + - - -
89C VAL* 2.8 29.8 + - + +
91C PHE* 3.8 22.0 - - + -
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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