Contacts of the strand formed by residues 91 - 99 (chain C) in PDB entry 3G33
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 GLU 91 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43C ARG* 3.7 35.6 + - + +
44C VAL 2.8 20.0 - - - +
45C PRO* 4.7 0.9 - - + -
46C ASN* 3.5 17.5 + - - +
86C SER* 4.3 1.0 - - - -
88C THR* 2.7 57.0 + - + +
89C ASP 3.4 1.2 + - - -
90C ARG* 1.3 84.3 - - - +
92C ILE* 1.3 59.8 + - - +
93C LYS* 4.7 4.0 + - - +
172C TYR* 3.3 23.7 + - - -
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Residues in contact with ILE 92 (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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142B VAL* 3.2 50.0 - - + -
150B TRP* 6.1 1.1 - - + -
43C ARG* 3.4 1.5 - - - -
44C VAL* 2.5 60.3 + - + +
45C PRO 4.8 2.0 - - - +
46C ASN* 3.9 14.1 - - + +
54C LEU* 5.3 3.8 - - + -
84C ALA* 4.6 1.8 - - + -
85C THR 3.3 27.4 - - - +
86C SER* 3.5 20.9 - - - +
87C ARG 5.1 0.4 - - - +
88C THR 5.6 0.4 - - - +
91C GLU* 1.3 76.1 - - - +
93C LYS* 1.3 59.8 + - - +
94C VAL* 4.1 13.0 - - + -
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Residues in contact with LYS 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41C SER* 5.8 6.5 - - - -
42C VAL 3.5 5.8 - - - +
43C ARG* 4.1 22.9 - - + +
83C CYS 3.9 0.5 - - - +
84C ALA* 3.5 2.6 - - - -
85C THR* 3.0 37.9 + - - +
87C ARG* 3.7 41.6 - - + +
88C THR* 3.4 26.7 + - - +
91C GLU* 4.7 8.1 + - - +
92C ILE* 1.3 73.2 - - - +
94C VAL* 1.3 61.9 + - - +
95C THR* 3.9 5.1 + - - +
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Residues in contact with VAL 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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150B TRP* 3.9 30.7 - - + -
40C LYS 3.7 1.0 - - - +
41C SER* 3.4 2.1 - - - -
42C VAL* 2.7 50.9 + - + +
44C VAL* 3.6 23.1 - - + -
58C THR* 5.7 1.1 - - + -
62C VAL* 5.4 4.5 - - + -
82C VAL* 3.9 20.6 - - + -
83C CYS 3.4 8.7 - - - +
84C ALA* 4.7 2.7 - - + -
92C ILE* 4.1 13.0 - - + -
93C LYS* 1.3 73.7 - - - +
95C THR* 1.3 65.6 + - - +
96C LEU* 3.9 10.7 + - + -
169C ILE* 6.4 0.2 - - + -
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Residues in contact with THR 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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10C ARG* 5.6 6.8 + - - -
39C LEU* 3.9 33.7 - - + -
40C LYS 3.5 10.8 - - - +
41C SER* 3.3 21.3 + - - +
82C VAL* 3.5 3.8 - - - +
83C CYS* 2.6 53.1 + - + +
93C LYS* 3.9 5.4 + - - +
94C VAL* 1.3 73.0 - - - +
96C LEU* 1.3 63.6 + - - +
97C VAL* 3.6 4.1 + - + +
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Residues in contact with LEU 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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38C ALA 3.4 5.7 - - - +
40C LYS* 2.7 57.5 + - + +
42C VAL* 4.1 21.3 - - + -
62C VAL* 4.5 21.5 - - + -
65C LEU* 5.0 1.3 - - + -
79C LEU* 3.8 22.2 - - + -
81C ASP 4.0 3.6 - - - -
82C VAL* 4.8 3.4 - - + +
94C VAL* 4.0 18.4 - - + +
95C THR* 1.3 70.9 - - - +
97C VAL* 1.3 60.9 + - - +
98C PHE* 3.4 31.3 + - + -
166C LEU* 4.4 15.3 - - + -
169C ILE* 4.8 5.4 - - + -
170C TYR* 4.9 2.2 - - + +
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Residues in contact with VAL 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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11C TYR* 3.7 39.5 - - + +
37C VAL* 3.7 34.5 - - + -
38C ALA 4.1 2.2 - - - -
39C LEU* 3.8 15.5 - - + -
79C LEU* 3.6 2.8 - - - +
80C MET* 2.8 30.1 + - + +
81C ASP* 2.8 32.3 + - + +
83C CYS* 4.3 8.1 - - - -
95C THR* 4.2 7.9 - - + +
96C LEU* 1.3 69.9 - - - +
98C PHE* 1.3 58.4 + - - +
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Residues in contact with PHE 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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37C VAL* 3.5 8.5 - - - +
38C ALA* 2.9 46.4 + - + +
40C LYS* 4.2 30.1 - - + -
65C LEU* 4.5 10.1 - - + -
77C VAL* 3.9 21.3 - - + -
78C ARG 3.5 13.9 - - - -
79C LEU* 3.9 24.5 - - + -
80C MET* 4.1 2.7 - - - -
96C LEU* 3.5 39.5 - - + -
97C VAL* 1.3 74.8 - - - +
99C GLU* 1.3 59.6 - - - +
100C HIS 3.4 0.7 + - - -
163C ASP 5.6 7.2 - - - -
164C PHE* 5.4 9.0 - + - -
166C LEU* 4.4 19.7 - - + -
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Residues in contact with GLU 99 (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 PHE 5.0 1.3 - - - -
37C VAL* 5.5 0.4 - - - -
38C ALA* 4.8 1.6 - - - +
76C VAL 4.0 2.9 - - - +
77C VAL* 3.4 25.5 - - + +
78C ARG* 2.7 58.8 + - + +
80C MET* 3.9 14.9 - - - +
98C PHE* 1.3 72.1 - - - +
100C HIS* 1.3 68.4 + - - +
101C VAL* 3.9 4.0 + - + +
152C LEU* 5.0 1.6 - - - +
160C LYS* 3.5 31.3 + - - +
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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