Contacts of the strand formed by residues 85 - 90 (chain C) in PDB entry 3F12
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 VAL 85 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36C TYR 3.4 2.1 - - - +
37C GLN* 3.6 0.2 - - - -
38C GLN* 2.8 45.0 + - + +
40C PRO* 6.4 1.6 - - + -
84C ALA* 1.3 79.1 - - - +
86C TYR* 1.3 62.2 + - - +
87C TYR* 3.4 38.5 - - + +
102C GLY* 4.0 1.1 - - - -
103C THR 3.8 22.0 - - - +
104C LYS* 3.5 33.2 - - + +
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Residues in contact with TYR 86 (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* 3.3 20.4 + - - +
21C LEU* 3.2 30.5 - - + -
35C TRP* 4.4 7.0 - + + -
36C TYR 3.0 5.6 - - - +
37C GLN* 3.6 40.0 + - + -
47C LEU* 3.9 20.2 - - + -
62C PHE* 4.2 1.3 - + - -
73C LEU* 4.1 7.0 - - + -
75C ILE* 3.7 20.6 - - + +
82C ASP* 2.6 42.1 + - - +
84C ALA* 3.4 24.0 + - + -
85C VAL* 1.3 72.0 - - - +
87C TYR* 1.3 61.2 + - - +
102C GLY 3.7 0.3 - - - -
103C THR* 3.4 19.6 + - - -
105C VAL* 4.0 10.3 - - + -
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Residues in contact with TYR 87 (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* 3.3 4.9 - - - -
35C TRP* 3.3 6.7 - - - -
36C TYR* 2.8 46.9 + - + +
38C GLN* 3.7 26.7 + - + -
44C PRO* 5.8 0.4 - - + -
85C VAL* 3.4 33.4 - - + +
86C TYR* 1.3 73.6 - - - +
88C CYS* 1.3 63.0 + - - +
99C PHE* 4.5 5.4 - + + -
100C GLY 4.3 7.6 - - - +
101C GLN 3.3 12.1 + - - -
102C GLY* 3.2 35.7 - - - -
39D GLN* 3.3 19.5 + - - -
43D LYS 4.7 1.9 + - - -
44D GLY* 4.4 11.0 - - - -
45D LEU* 3.6 34.1 - - + -
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Residues in contact with CYS 88 (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 LEU* 3.9 20.9 - - - -
6C GLN* 3.2 17.3 + - - -
23C CYS* 2.0 48.7 - - - -
33C LEU* 3.8 17.3 - - + -
34C ALA 3.1 10.5 - - - +
35C TRP* 4.2 6.7 - - + -
87C TYR* 1.3 74.7 - - - +
89C GLN* 1.3 61.5 + - - +
99C PHE* 3.4 2.6 - - - -
100C GLY* 2.5 34.0 + - - -
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Residues in contact with GLN 89 (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 LEU* 4.0 2.9 - - - -
32C TYR 3.8 0.5 - - - +
33C LEU* 3.7 2.6 - - - -
34C ALA* 2.9 34.9 + - - +
36C TYR* 2.9 35.0 + - + -
88C CYS* 1.3 76.4 - - - +
90C GLN* 1.3 87.1 + - - +
91C ARG* 4.0 2.5 - - - +
97C TRP* 3.9 15.6 - - + +
98C THR 2.9 22.4 - - - +
99C PHE* 3.5 27.6 - - + -
110D GLY 3.2 25.9 + - - +
111D LEU* 4.8 0.3 - - - -
112D LEU* 3.5 8.1 - - - +
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Residues in contact with GLN 90 (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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2C ILE* 3.1 25.8 - - - +
4C LEU* 3.6 18.2 - - + +
29C VAL* 3.7 26.7 - - + -
32C TYR 3.2 9.4 - - - +
33C LEU* 4.4 10.8 - - + +
89C GLN* 1.3 96.4 + - - +
91C ARG* 1.3 64.3 + - - +
92C SER 3.4 14.3 - - - +
93C ASN 3.3 25.5 + - - +
94C TRP* 5.2 0.2 - - - +
96C PRO 4.8 0.2 + - - -
97C TRP* 4.4 3.3 - - - +
98C THR* 2.6 35.9 + - - +
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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