Contacts of the strand formed by residues 91 - 98 (chain C) in PDB entry 3W12
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 ALA 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C ARG* 4.1 10.8 - - + +
39C GLN 3.5 12.3 - - - +
40C PRO* 3.5 25.6 - - + -
41C PRO* 4.6 3.6 - - - -
89C ASP 3.2 5.3 + - - +
90C THR* 1.3 76.3 - - - +
92C ARG* 1.3 60.7 + - - +
93C TYR* 3.3 20.7 - - + -
113C SER* 5.1 1.8 - - - -
114C VAL 3.0 32.3 + - - +
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Residues in contact with ARG 92 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL 3.9 0.3 - - - +
38C ARG* 3.0 5.5 - - - -
39C GLN* 2.7 43.8 + - + +
41C PRO* 5.4 0.8 - - - +
91C ALA* 1.3 71.1 - - - +
93C TYR* 1.3 61.8 + - - +
94C TYR* 3.5 35.4 + - + +
110C GLN* 2.8 22.0 + - - +
111C GLY* 2.6 30.7 + - - -
112C THR 3.5 16.0 - - - +
113C SER* 4.4 20.6 - - - +
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Residues in contact with TYR 93 (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 GLU* 3.6 4.5 - - - +
18C LEU* 4.0 17.8 - - + +
20C ILE* 3.8 28.5 - - + -
36C TRP* 5.3 4.7 - + + -
37C VAL 3.6 2.0 - - - +
38C ARG* 3.3 41.8 + - + -
48C LEU* 3.9 17.9 - - + -
80C LEU* 5.3 5.2 - - + -
82C MET* 4.5 8.1 - - - +
85C LEU* 4.7 0.2 - - - +
89C ASP* 2.8 31.5 + - - +
91C ALA* 3.3 25.4 - - + -
92C ARG* 1.3 73.6 - - - +
94C TYR* 1.3 60.7 + - - +
111C GLY* 3.6 1.0 - - - -
112C THR* 2.9 40.2 + - + +
114C VAL* 3.7 22.9 - - + -
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Residues in contact with TYR 94 (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 GLU* 3.1 6.3 - - - +
36C TRP* 3.3 10.3 - - - -
37C VAL* 2.7 57.6 + - + +
38C ARG 5.0 0.2 - - - -
39C GLN* 4.0 20.9 + - + -
45C LEU* 5.1 5.8 - - + -
92C ARG* 3.5 32.9 - - + +
93C TYR* 1.3 72.3 - - - +
95C CYS* 1.3 68.5 + - - +
108C TRP* 4.3 18.8 - + + -
109C GLY 3.6 12.6 - - - -
110C GLN 3.6 9.4 - - - -
111C GLY* 3.4 19.7 - - - -
44D GLN* 3.9 17.0 + - - -
48D GLN 4.8 1.4 + - - -
49D SER* 3.6 27.3 - - - -
50D PRO* 4.5 9.4 - - + -
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Residues in contact with CYS 95 (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 13.8 - - - +
5C LYS 4.8 0.4 - - - -
6C GLU* 3.3 20.1 + - - +
22C CYS* 2.0 53.4 - - + -
34C VAL* 4.1 8.3 - - + -
35C ASN 2.9 11.2 - - - +
36C TRP* 3.7 10.8 - - + -
37C VAL* 6.1 0.4 - - - -
94C TYR* 1.3 77.5 - - - +
96C ALA* 1.3 62.4 + - - +
109C GLY 3.2 23.4 + - - -
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Residues in contact with ALA 96 (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 5.8 - - - -
34C VAL* 3.6 1.6 - - - -
35C ASN* 2.8 34.7 + - + +
37C VAL* 5.5 1.5 - - + +
95C CYS* 1.3 77.1 - - - +
97C ARG* 1.3 64.4 + - - +
105C MET* 3.7 25.1 - - + -
107C TYR 3.6 12.8 - - - +
108C TRP* 3.7 26.0 - - + -
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Residues in contact with ARG 97 (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 VAL* 3.6 28.7 - - - +
4C LEU* 3.7 9.1 - - + +
27C PHE* 3.4 51.8 - - + +
32C TYR* 3.4 46.3 + - + -
33C GLY 3.8 8.1 - - - +
34C VAL* 4.7 1.3 - - - +
96C ALA* 1.3 73.8 - - - +
98C ASP* 1.3 70.8 + - - +
99C PRO* 4.8 1.4 - - - +
105C MET* 3.2 27.2 - - - +
106C ASP* 2.6 53.2 + - - +
107C TYR* 3.0 21.9 + - + +
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Residues in contact with ASP 98 (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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32C TYR* 3.8 2.6 - - - +
33C GLY* 2.9 45.4 + - - +
35C ASN* 2.8 21.9 + - - +
50C MET* 3.3 13.9 - - + +
97C ARG* 1.3 80.4 - - - +
99C PRO* 1.3 60.3 - - - +
100C TYR* 3.0 19.6 + - - -
103C LYS 3.9 0.2 - - - +
104C PRO 3.1 9.4 - - - +
101D ARG* 2.7 44.2 + - - -
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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