Contacts of the strand formed by residues 31 - 37 (chain C) in PDB entry 3OF6
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 SER 31 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C HIS* 4.3 1.6 - - - +
30C VAL* 1.3 81.3 - - - +
32C LEU* 1.3 62.3 + - - +
33C PHE* 3.7 12.3 - - - -
48C TYR* 3.0 23.4 + - - -
49C PHE 3.5 6.3 - - - -
69C ARG* 4.7 1.4 + - - -
93C ALA 4.3 0.2 - - - -
94C SER* 3.2 25.2 - - - -
95C SER* 3.2 30.4 + - - -
96C LEU 4.6 0.9 + - - -
97C GLY* 4.0 14.9 - - - -
98C GLN 4.0 1.2 + - - -
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Residues in contact with LEU 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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25C PRO* 3.6 18.6 - - + -
31C SER* 1.3 75.6 - - - +
33C PHE* 1.3 69.9 + - - +
34C TRP* 3.4 30.5 - - + +
47C THR 4.2 0.2 - - - +
48C TYR* 3.7 4.1 - - - -
49C PHE* 2.8 41.9 + - + +
69C ARG* 3.3 25.8 - - - +
73C SER 3.4 24.0 - - - +
75C SER* 3.4 23.1 - - - +
92C CYS* 3.8 10.5 - - - -
93C ALA 3.2 8.7 - - - +
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Residues in contact with PHE 33 (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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31C SER* 3.7 13.9 - - - -
32C LEU* 1.3 77.6 - - - +
34C TRP* 1.3 73.7 + - - +
35C TYR* 3.5 34.5 - - + -
45C PHE* 4.3 13.9 - + + -
47C THR 3.8 4.3 - - - +
48C TYR* 3.3 36.3 - + - -
92C CYS* 3.5 4.9 - - - -
93C ALA* 3.0 44.8 + - + -
95C SER* 3.5 23.6 - - - -
98C GLN* 4.9 19.5 - - + -
106C GLN* 4.3 18.4 - - + -
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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* 4.4 13.2 - - - -
21C LEU* 4.2 20.6 - - + -
22C ARG 4.9 0.2 - - - -
23C CYS* 3.8 28.0 - - + -
32C LEU* 3.4 13.2 - - + +
33C PHE* 1.3 88.0 - - - +
35C TYR* 1.3 66.2 + - - +
45C PHE* 3.7 2.3 - - - -
46C LEU* 2.8 44.6 + - + -
47C THR* 3.4 30.1 + - + +
49C PHE* 4.6 2.9 - + - -
67C ALA* 4.4 4.7 - - + +
75C SER* 3.2 22.8 + - - -
77C LEU* 3.8 45.8 - - + -
90C TYR* 4.1 22.4 - - + -
91C LEU 3.2 23.6 - - - -
92C CYS* 4.6 1.3 - - + -
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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 PHE* 3.5 36.6 - + + -
34C TRP* 1.3 75.9 - - - +
36C GLN* 1.3 61.1 + - - +
37C GLN 4.3 0.7 - - - -
43C PRO* 3.6 41.1 - - + -
44C GLU 3.4 3.6 - - - -
45C PHE* 3.8 29.3 - + + -
46C LEU* 3.5 9.2 - - - +
90C TYR* 3.4 6.2 - - - +
91C LEU* 3.0 41.5 + - + +
93C ALA* 4.4 1.6 - - + -
106C GLN* 3.5 32.7 + - - -
108C PHE* 3.8 20.2 - + - -
46E TRP* 4.1 20.2 - + + -
54E ALA* 5.2 4.3 - - + -
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Residues in contact with GLN 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 78.0 - - - +
37C GLN* 1.3 65.5 + - - +
38C ALA* 4.1 6.8 + - + +
42C GLY 3.7 3.3 - - - +
44C GLU* 2.9 48.3 + - + +
46C LEU* 3.8 26.7 - - + +
61C PRO* 4.6 11.4 - - - +
65C PHE* 5.5 6.0 - - - -
85C GLU 4.5 12.3 + - - -
86C ASP* 5.2 0.8 - - - +
88C ALA* 4.1 17.5 - - + +
89C VAL 4.0 2.0 - - - -
90C TYR* 3.9 31.5 + - + -
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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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36C GLN* 1.3 75.3 - - - +
38C ALA* 1.3 60.4 + - - +
40C GLY* 6.1 0.7 - - - -
41C GLN 3.9 15.9 + - - +
43C PRO* 3.2 39.2 - - + +
88C ALA* 3.2 3.8 - - - +
89C VAL* 3.0 44.0 + - + +
91C LEU* 3.3 28.9 - - + +
42E ASP* 4.8 9.0 + - - +
44E PRO* 3.5 20.4 - - - +
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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