Contacts of the strand formed by residues 102 - 113 (chain C) in PDB entry 2V10
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 ILE 102 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6C THR* 4.9 3.4 - - + -
8C SER* 4.0 22.7 - - - +
98C THR* 3.5 1.2 - - - -
99C VAL* 2.9 34.7 + - + +
100C GLY 3.2 0.2 - - - -
101C GLY* 1.4 75.5 - - - +
103C THR* 1.3 66.6 + - - +
104C VAL* 3.9 18.3 + - + -
147C ILE* 4.0 28.7 - - + -
150C GLN* 4.9 9.2 - - + +
152C VAL* 4.7 16.4 - - + -
153C LEU* 4.3 13.9 - - + -
178C LEU* 4.3 19.3 - - + -
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Residues in contact with THR 103 (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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96C ILE* 4.4 19.6 - - + +
97C ILE 3.5 6.7 - - - +
98C THR* 3.2 22.2 + - - +
101C GLY 4.0 2.6 + - - -
102C ILE* 1.3 74.6 - - - +
104C VAL* 1.3 70.8 + - - +
105C THR* 6.2 0.2 - - + -
150C GLN* 3.4 20.8 + - - -
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Residues in contact with VAL 104 (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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96C ILE* 3.2 4.8 - - - +
97C ILE* 2.6 51.6 + - + +
99C VAL* 5.3 1.6 - - + -
102C ILE* 4.0 8.3 - - + +
103C THR* 1.3 82.4 - - - +
105C THR* 1.4 57.7 + - - +
106C GLN* 4.1 12.3 - - + +
143C ILE* 4.2 13.5 - - + -
146C ASN* 4.6 8.5 - - + -
147C ILE* 3.3 44.0 - - + +
150C GLN* 4.3 13.0 - - - +
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Residues in contact with THR 105 (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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71C SER 6.0 1.1 - - - +
73C LYS* 6.5 0.4 - - - -
94C GLN* 3.6 23.2 + - - +
95C ASP* 3.4 6.3 - - - +
96C ILE* 3.0 32.1 - - + +
103C THR* 6.2 0.2 - - + -
104C VAL* 1.4 70.4 - - - +
106C GLN* 1.3 61.1 + - - +
146C ASN* 4.1 12.8 + - - -
150C GLN* 5.4 0.6 + - - -
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Residues in contact with GLN 106 (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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44C VAL* 4.2 12.8 - - + +
94C GLN* 3.3 14.7 - - - +
95C ASP 3.1 18.9 + - - +
97C ILE* 3.7 28.0 - - + -
104C VAL* 3.9 11.4 - - + -
105C THR* 1.3 76.8 - - - +
107C MET* 1.3 90.7 + - - +
108C PHE* 3.7 5.1 - - - -
140C VAL* 4.5 0.6 - - - +
141C THR 3.1 19.3 + - - +
142C PRO* 4.5 0.4 - - - +
143C ILE* 3.4 29.3 + - + +
146C ASN* 2.2 34.1 + - - +
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Residues in contact with MET 107 (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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43C ASN* 5.7 1.2 + - - -
44C VAL* 4.6 3.6 + - - +
74C HIS 5.6 0.2 - - - +
75C ASN* 4.4 24.9 - - + +
92C LEU* 4.9 12.8 - - + -
93C SER 3.2 21.5 - - - +
94C GLN* 3.2 49.4 - - + +
106C GLN* 1.3 87.9 + - - +
108C PHE* 1.3 60.9 + - - +
140C VAL* 3.3 31.0 - - + +
141C THR 5.0 0.9 - - - +
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Residues in contact with PHE 108 (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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26C ILE* 3.4 30.1 - - + -
43C ASN* 6.1 0.9 - - - +
44C VAL* 3.3 33.0 - - + +
46C VAL* 4.2 21.1 - - + -
64C PHE* 3.9 26.9 - + - -
72C TYR* 5.5 0.2 - + - -
79C LEU* 5.1 0.2 - - - -
92C LEU* 3.1 10.8 - - - +
93C SER* 2.7 52.8 + - - -
94C GLN 4.1 0.2 - - - -
95C ASP* 3.7 21.3 - - + -
97C ILE* 4.0 15.0 - - + -
106C GLN 3.7 12.3 - - - -
107C MET* 1.3 75.9 - - - +
109C GLY* 1.3 70.3 + - - +
110C GLU* 4.4 6.1 - - + -
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Residues in contact with GLY 109 (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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43C ASN* 5.9 0.2 - - - +
44C VAL 2.8 15.1 + - - -
45C TRP* 2.8 10.2 - - - +
46C VAL 2.8 31.4 + - - +
79C LEU* 4.1 10.0 - - - +
91C PHE 3.3 8.7 - - - -
92C LEU* 3.9 7.2 - - - +
108C PHE* 1.3 81.1 - - - +
110C GLU* 1.3 58.5 + - - -
111C VAL* 5.2 0.9 - - - -
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Residues in contact with GLU 110 (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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46C VAL 3.5 5.6 - - - +
48C SER* 2.6 31.1 + - - +
49C SER* 4.2 2.8 + - - -
50C LYS* 5.2 2.1 - - - +
64C PHE* 3.1 43.2 - - + +
66C ALA* 4.5 5.8 + - - +
72C TYR* 4.2 6.4 + - - -
90C GLY* 3.4 1.6 - - - -
91C PHE* 2.9 54.0 + - + +
93C SER* 2.8 25.6 + - - +
108C PHE* 4.1 5.3 + - + -
109C GLY* 1.3 71.2 - - - -
111C VAL* 1.3 59.9 + - - +
112C THR* 3.9 3.1 + - - +
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Residues in contact with VAL 111 (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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45C TRP* 3.7 34.8 - - + -
46C VAL 3.1 12.1 + - - +
47C PRO* 3.7 4.3 - - + +
48C SER 3.0 21.5 + - - +
51C CYS* 3.8 4.0 - - - +
81C LEU* 5.6 1.3 - - + -
88C VAL* 3.8 19.7 - - + -
89C SER 3.2 13.7 - - - +
90C GLY* 3.9 0.7 - - - -
109C GLY 5.2 0.4 - - - -
110C GLU* 1.3 67.8 - - - +
112C THR* 1.3 63.2 + - - +
113C GLU 2.8 35.2 - - - +
114C MET* 3.7 17.3 - - + -
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Residues in contact with THR 112 (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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48C SER* 3.6 21.8 - - - +
50C LYS* 4.1 15.4 + - + +
51C CYS* 3.4 36.7 - - - +
52C SER* 4.3 2.1 + - - -
55C TYR* 4.1 7.8 - - - -
89C SER 3.2 2.6 + - - -
90C GLY* 4.0 7.8 - - - -
91C PHE* 4.1 18.7 - - + -
110C GLU 3.9 8.0 + - - +
111C VAL* 1.3 75.3 - - - +
113C GLU* 1.3 75.8 + - - +
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Residues in contact with GLU 113 (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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55C TYR* 3.2 29.2 + - + +
78C GLU* 5.7 0.5 - - - +
88C VAL* 3.4 3.3 - - - -
89C SER* 3.0 41.8 + - - +
90C GLY* 5.0 0.5 + - - -
111C VAL* 2.8 17.1 - - - +
112C THR* 1.3 96.8 + - - +
114C MET* 1.3 58.1 + - - +
115C PRO* 4.1 4.0 - - + -
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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