Contacts of the helix formed by residues 92 - 103 (chain C) in PDB entry 2V1C
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
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Residue Dist Surf HB Arom Phob DC
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53C PHE* 3.7 29.4 - - + -
83C LEU* 4.9 5.8 - - + -
88C ARG 3.6 3.0 + - - -
89C TYR 2.9 8.4 + - - +
91C PHE* 1.3 83.5 - - - +
93C HIS* 1.3 52.9 + - - +
94C LEU 3.3 0.7 - - - -
95C MET* 2.8 6.0 + - - +
96C ALA* 2.4 37.9 + - - +
120C LEU* 3.5 24.2 - - + +
123C VAL* 4.0 8.3 - - + +
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Residues in contact with HIS 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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112A SER* 1.9 48.3 + - - -
113A PRO* 2.5 32.6 + - + -
146A GLU* 2.9 26.8 + - - -
52C LEU* 4.2 12.9 - - + +
53C PHE* 4.0 10.1 - + - -
89C TYR* 3.7 15.5 + + - +
90C ALA* 5.0 5.4 - - - +
91C PHE 4.6 0.2 - - - +
92C ALA* 1.3 73.0 - - - +
94C LEU* 1.4 55.5 + - - +
96C ALA* 4.6 2.5 - - - -
97C GLU* 2.3 49.6 + - - +
235C LEU* 3.2 17.2 - - + +
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Residues in contact with LEU 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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90C ALA 4.3 9.3 + - - +
91C PHE* 4.8 10.8 - - + +
93C HIS* 1.4 78.1 - - - +
95C MET* 1.3 58.2 + - + +
98C PHE* 2.4 45.1 + - + +
137C SER* 5.4 1.3 - - - +
215C TRP* 3.4 39.7 - - + -
232C TRP* 2.8 35.7 - - + +
235C LEU* 2.6 65.4 - - + +
236C VAL* 3.7 5.6 - - + -
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Residues in contact with MET 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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91C PHE 3.2 18.8 + - - +
92C ALA* 2.8 13.7 + - - +
94C LEU* 1.3 85.4 - - + +
96C ALA* 1.3 57.0 + - - +
98C PHE* 3.6 5.6 - - - +
99C ALA* 2.9 31.5 + - - +
116C PHE* 3.7 7.6 - - + -
119C SER* 3.0 32.8 - - - +
120C LEU* 4.2 6.7 - - + -
123C VAL* 5.2 0.2 - - + -
133C ALA* 3.0 50.9 - - + +
136C MET* 4.3 11.7 - - - -
137C SER* 3.5 20.6 - - - +
140C LEU* 5.0 4.6 - - + +
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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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13C ILE* 3.7 42.6 - - + +
53C PHE* 4.2 13.9 - - + -
92C ALA 2.4 28.0 + - - +
93C HIS* 3.6 2.9 - - - +
95C MET* 1.3 65.1 - - - +
97C GLU* 1.3 66.9 + - + +
99C ALA* 3.4 2.5 + - - +
100C ASP* 3.1 25.5 + - - +
116C PHE* 3.6 16.0 - - + -
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Residues in contact with GLU 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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113A PRO 4.4 6.3 - - - +
114A MET* 3.8 23.9 - - + +
13C ILE 4.6 6.1 - - - +
14C ARG* 2.8 48.8 + - - +
93C HIS* 2.3 47.9 + - - +
96C ALA* 1.3 70.8 - - + +
98C PHE* 1.3 59.0 + - - +
100C ASP* 3.6 2.8 + - - +
101C ALA* 3.2 23.7 + - - +
231C SER* 4.7 7.1 + - - -
232C TRP* 3.6 11.8 - - + +
235C LEU* 3.0 20.9 - - + -
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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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94C LEU* 2.4 34.7 + - + +
95C MET* 3.6 3.8 - - - +
97C GLU* 1.3 74.0 - - - +
99C ALA* 1.3 58.7 + - - +
101C ALA* 3.2 4.0 + - - +
102C LEU* 2.9 47.8 + - + +
137C SER* 3.3 53.8 - - - +
140C LEU* 4.2 12.1 - - + -
141C LEU* 3.7 17.3 - - + -
218C LEU* 4.2 8.7 - - + -
222C VAL* 4.2 15.5 - - + -
232C TRP* 3.7 50.6 - + + +
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Residues in contact with ALA 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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28C LEU* 3.9 23.6 - - + -
95C MET 2.9 17.5 + - - +
96C ALA 3.8 3.6 - - - +
98C PHE* 1.3 79.4 - - - +
100C ASP* 1.3 62.5 + - - +
102C LEU* 3.3 5.6 + - - -
103C PHE* 3.2 39.9 + - + +
108C PHE* 6.0 0.7 - - + -
116C PHE* 4.1 12.6 - - + -
140C LEU* 4.5 10.8 - - + -
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Residues in contact with ASP 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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13C ILE* 4.0 20.9 - - + +
14C ARG* 2.9 33.9 + - - +
26C THR* 4.6 6.6 - - - +
28C LEU* 4.9 7.7 - - - +
96C ALA 3.1 18.4 + - - +
97C GLU 3.9 4.3 - - - +
99C ALA* 1.3 76.2 - - - +
101C ALA* 1.3 61.8 + - - +
103C PHE 3.3 16.5 - - - +
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Residues in contact with ALA 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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97C GLU 3.2 14.4 + - - +
98C PHE 3.2 3.2 + - - +
100C ASP* 1.3 78.5 - - - +
102C LEU* 1.3 64.9 + - - +
103C PHE 3.4 3.3 + - - +
104C GLN* 5.2 1.4 - - - +
222C VAL* 6.1 0.2 - - + -
226C VAL* 3.8 15.6 - - - +
227C GLY 4.8 2.6 - - - +
230C HIS* 3.9 18.0 - - + +
231C SER 5.8 0.4 - - - +
232C TRP* 3.6 24.7 - - + +
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Residues in contact with LEU 102 (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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98C PHE* 2.9 41.8 + - + +
99C ALA 3.3 4.9 + - - +
101C ALA* 1.3 80.2 - - - +
103C PHE* 1.3 64.8 + - + +
104C GLN* 3.8 3.6 + - - +
107C GLU* 4.1 5.4 - - - +
140C LEU* 3.7 37.2 - - + +
141C LEU* 3.9 20.6 - - + -
144C ALA* 3.9 17.6 - - + +
146C VAL* 4.7 6.8 - - + +
222C VAL* 4.6 9.9 - - + -
226C VAL* 4.1 31.4 - - + +
230C HIS* 5.6 1.1 - - - -
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Residues in contact with PHE 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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99C ALA* 3.2 31.3 + - + +
100C ASP* 3.3 15.6 - - - +
101C ALA 4.3 1.7 - - - +
102C LEU* 1.3 92.0 - - + +
104C GLN* 1.3 61.0 + - - +
105C GLU* 3.3 6.7 + - - +
107C GLU* 3.3 31.2 - - + +
108C PHE* 3.8 37.9 - + + -
112C ALA* 3.9 17.7 - - + -
140C LEU* 4.1 24.9 - - + -
143C LEU* 3.5 24.0 - - + -
144C ALA* 3.7 16.6 - - + -
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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