Contacts of the strand formed by residues 92 - 103 (chain C) in PDB entry 3VG9
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 92 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C LYS* 3.7 32.8 - - + -
39C GLN 3.1 15.5 - - - +
40C SER* 4.0 4.5 - - - +
41C HIS 5.8 0.9 - - - +
90C ASP 3.3 2.6 + - - -
91C SER* 1.3 77.8 - - - +
93C VAL* 1.3 65.9 + - - +
94C TYR* 3.8 9.4 - - + -
118C THR 3.9 0.3 - - - +
119C THR* 3.8 3.9 - - - +
120C LEU* 2.9 31.0 + - - +
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Residues in contact with VAL 93 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C VAL 3.8 0.7 - - - +
38C LYS* 3.7 1.6 - - - -
39C GLN* 2.9 40.4 + - + +
92C ALA* 1.3 77.9 - - - +
94C TYR* 1.3 64.4 + - - +
95C TYR* 3.8 31.7 + - + +
117C GLY* 4.1 3.8 - - - -
118C THR 3.3 22.4 - - - +
119C THR* 3.6 23.8 - - + +
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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
----------------------------------------------------------
6C GLN* 2.7 25.3 + - - -
20C ILE* 4.2 20.4 - - + -
36C TRP* 4.5 11.4 - - + -
37C VAL 3.4 1.3 - - - +
38C LYS* 3.6 29.7 + - + +
48C ILE* 3.5 33.2 - - + -
64C PHE* 5.9 0.7 - + - -
81C ILE* 4.9 3.8 - - + -
83C LEU* 4.2 28.3 - - + +
90C ASP* 2.5 39.0 + - - +
92C ALA* 3.8 13.7 - - + -
93C VAL* 1.3 75.4 - - - +
95C TYR* 1.3 56.0 + - - +
117C GLY* 3.5 0.9 - - - -
118C THR 2.8 29.2 + - - +
120C LEU* 4.0 21.7 - - + +
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Residues in contact with TYR 95 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B GLN* 3.3 17.7 + - - -
42B GLY 3.3 9.5 + - - -
43B SER* 3.1 28.0 - - - -
44B PRO* 3.9 10.3 - - + -
6C GLN* 3.6 1.3 - - - +
36C TRP* 3.1 12.3 - - - -
37C VAL* 2.9 41.3 + - + +
39C GLN* 3.4 27.6 + - + -
45C LEU* 4.9 0.7 - - + -
93C VAL* 3.8 25.5 - - + +
94C TYR* 1.3 76.5 - - - +
96C CYS* 1.3 59.6 + - - +
114C TRP* 3.9 32.3 - + + -
115C GLY 3.4 17.3 - - - -
116C GLN 3.9 2.1 + - - -
117C GLY* 3.7 15.3 - - - -
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Residues in contact with CYS 96 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 3.7 12.5 - - - +
6C GLN* 3.5 18.1 + - - +
22C CYS* 2.0 54.7 - - + -
34C MET* 3.9 7.9 - - + -
35C ASN 3.2 9.4 - - - +
36C TRP* 3.7 17.3 - - + -
95C TYR* 1.3 77.0 - - - +
97C ALA* 1.3 60.3 + - - +
114C TRP* 3.6 2.9 - - - +
115C GLY 2.9 26.5 + - - -
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Residues in contact with ALA 97 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C LEU* 4.1 0.2 - - - -
34C MET* 3.3 11.1 - - - +
35C ASN* 2.9 34.2 + - + +
37C VAL* 5.2 2.0 - - + -
95C TYR 4.0 0.4 + - - -
96C CYS* 1.3 74.6 - - - +
98C ARG* 1.3 59.7 + - - +
111C PHE* 3.6 39.3 - - + -
113C TYR 3.3 6.7 - - - +
114C TRP* 3.9 21.3 - - + -
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Residues in contact with ARG 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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2C VAL* 4.3 12.2 - - - +
4C LEU* 4.2 10.3 - - + -
24C THR* 5.5 4.9 - - - -
27C ASP* 3.0 36.6 + - - +
28C SER 5.0 2.4 + - - -
32C TYR* 3.5 47.6 - - + -
33C ASN 3.9 2.0 - - - -
34C MET* 4.1 17.3 - - - -
97C ALA* 1.3 72.9 - - - +
99C GLU* 1.3 61.4 + - - +
100C GLY* 5.8 0.2 - - - -
111C PHE* 3.1 6.2 - - - -
112C ASP* 2.9 61.4 + - - +
113C TYR* 2.8 41.2 + - + +
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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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91B PHE* 4.5 4.5 - - + -
96B TRP* 3.1 29.6 - - - -
32C TYR* 3.1 28.9 - - - +
33C ASN* 3.1 28.6 + - + +
35C ASN* 3.4 13.3 + - - +
50C ASN* 3.3 17.7 + - - -
59C ARG* 5.9 0.5 + - - -
97C ALA 4.1 0.6 + - - -
98C ARG* 1.3 72.6 - - - +
100C GLY* 1.3 67.0 + - - +
101C ASN* 3.1 16.0 + - - +
109C ARG* 3.0 25.2 - - - -
110C TYR 3.2 9.6 - - - +
111C PHE* 4.0 9.9 - - + -
112C ASP* 4.5 1.1 - - - -
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Residues in contact with GLY 100 (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* 4.4 6.7 - - - -
98C ARG* 3.7 2.4 + - - -
99C GLU* 1.3 74.5 - - - +
101C ASN* 1.3 65.9 + - - -
109C ARG* 3.3 24.9 - - - -
110C TYR* 2.7 43.5 + - - -
112C ASP* 4.2 6.7 + - - -
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Residues in contact with ASN 101 (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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224A THR* 5.3 1.0 - - - +
228A GLU* 4.9 0.3 - - - +
32C TYR* 4.4 16.3 + - + -
33C ASN* 4.9 6.7 - - - +
99C GLU* 3.1 31.9 + - - +
100C GLY* 1.3 78.5 + - - -
102C TYR* 1.3 68.5 + - - +
107C SER* 4.9 8.1 - - - -
108C VAL 3.2 5.1 + - - +
109C ARG* 3.9 16.3 + - - +
110C TYR* 4.0 4.8 + - - -
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Residues in contact with TYR 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A THR* 3.8 23.1 - - + -
227A LYS* 3.3 42.6 - - + +
228A GLU* 3.3 31.9 - - + +
49B TYR* 3.6 17.3 - + - -
50B ALA* 4.7 0.2 - - - +
53B ASN* 3.6 11.4 + - - -
101C ASN* 1.3 77.6 + - - +
103C TYR* 1.3 68.0 + - - +
104C ASP* 3.8 16.4 + - + +
106C GLY 3.5 0.5 - - - +
107C SER* 3.7 2.8 - - - -
108C VAL* 2.7 72.5 + - + +
110C TYR* 3.8 12.1 - + - -
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Residues in contact with TYR 103 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ASN* 3.5 29.2 - - - -
41A THR* 3.6 23.8 - - + +
42A ASN* 2.7 20.7 + - - -
45A VAL* 4.7 1.7 - - - +
102A ARG* 3.4 39.9 + - - +
228A GLU* 3.7 17.7 + - - +
231A ALA* 3.5 16.8 - - + +
235A LEU* 3.8 24.0 - - + +
292A ILE* 5.3 1.8 - - + +
295A PHE* 4.6 5.0 - - - -
102C TYR* 1.3 76.3 - - - +
104C ASP* 1.3 58.7 + - - +
105C GLY* 3.1 38.3 - - - -
106C GLY 3.4 8.1 - - - -
107C SER* 5.1 1.6 - - - +
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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