Contacts of the helix formed by residues 95 - 112 (chain C) in PDB entry 2YVC
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 GLN 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C GLY 2.7 27.8 + - - -
39C LEU* 3.4 4.1 - - - -
40C ARG* 2.5 44.6 + - + +
41C GLU* 2.7 27.6 + - - +
94C ILE* 1.3 75.3 - - + +
96C GLU* 1.3 68.3 + - - +
97C ILE* 4.0 5.4 - - - +
98C THR* 3.5 9.6 + - - +
99C GLN* 3.2 24.4 + - - +
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Residues in contact with GLU 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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94C ILE 3.9 1.2 + - - -
95C GLN* 1.3 72.7 - - - +
97C ILE* 1.3 66.4 + - + +
99C GLN* 3.1 6.6 + - - +
100C ARG* 2.5 45.4 + - - +
184C ARG* 2.9 23.8 + - - +
185C GLU* 2.7 47.9 + - - +
188C MET* 4.0 9.2 - - - +
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Residues in contact with ILE 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 THR* 5.9 0.2 - - - +
13C ASP* 5.1 3.8 - - - +
37C VAL* 3.8 34.8 - - + +
38C GLY 3.4 26.5 - - - +
39C LEU* 3.9 16.6 - - + -
95C GLN* 4.0 10.1 - - - +
96C GLU* 1.3 80.3 - - + +
98C THR* 1.3 54.2 + - - +
100C ARG* 3.1 33.5 + - - +
101C LEU* 2.8 59.9 + - + +
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Residues in contact with THR 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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39C LEU* 3.1 17.5 - - - +
41C GLU* 3.1 42.1 + - + +
44C PHE* 4.9 0.7 - - + -
45C PHE* 4.2 14.4 - - + -
93C LEU* 3.6 31.4 - - + -
95C GLN* 3.5 7.9 - - - +
96C GLU 3.2 0.4 - - - -
97C ILE* 1.3 74.6 - - - +
99C GLN* 1.3 67.2 + - - +
101C LEU* 3.1 5.8 + - - +
102C PHE* 3.0 31.9 + - + +
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Residues in contact with GLN 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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93C LEU* 3.9 23.6 + - + +
94C ILE 3.4 17.2 + - - -
95C GLN 3.2 19.1 + - - +
96C GLU* 3.1 6.6 + - - +
98C THR* 1.3 79.0 - - - +
100C ARG* 1.3 57.3 + - - +
102C PHE* 3.5 1.0 + - - +
103C PHE* 2.9 32.9 + - - +
185C GLU* 3.3 36.3 + - - +
188C MET* 4.4 13.9 - - + -
189C MET* 3.3 45.4 + - + +
192C LEU* 4.0 2.1 - - - +
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Residues in contact with ARG 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 ASP* 2.8 25.0 + - - +
37C VAL* 5.6 0.8 - - - +
96C GLU* 2.5 46.8 + - - +
97C ILE* 3.1 35.8 + - + +
99C GLN* 1.3 77.0 - - - +
101C LEU* 1.3 57.5 + - - +
103C PHE* 3.8 1.4 - - + +
104C LEU* 2.9 52.7 + - + +
184C ARG* 3.1 21.3 - - - +
188C MET* 3.8 23.0 - - + -
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C THR* 3.6 26.2 - - + +
12C MET* 3.8 28.0 - - + +
13C ASP* 4.8 6.5 - - - +
37C VAL* 5.5 2.9 - - + -
39C LEU* 4.4 5.2 - - + -
45C PHE* 4.0 22.9 - - + -
80C PHE* 3.5 34.5 - - + +
82C ALA* 5.5 0.4 - - - +
97C ILE* 2.8 46.5 + - + +
98C THR 3.1 3.6 + - - +
100C ARG* 1.3 73.6 - - - +
102C PHE* 1.3 61.3 + - - +
104C LEU* 5.2 0.2 - - + -
105C GLN* 3.4 24.6 + - - +
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Residues in contact with PHE 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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44C PHE* 3.9 15.9 - + + -
45C PHE* 4.2 12.8 - + - -
82C ALA* 3.5 23.8 - - + -
84C PHE 3.4 21.1 - - - -
85C PHE* 3.6 35.4 - + - -
86C PRO* 3.6 12.8 - - + -
89C VAL* 5.5 0.7 - - + -
93C LEU* 3.3 44.4 - - + -
98C THR* 3.0 17.9 + - + +
99C GLN 4.0 0.9 - - - +
101C LEU* 1.3 73.9 - - - +
103C PHE* 1.3 67.5 + - - +
104C LEU 3.0 2.0 + - - -
105C GLN* 3.0 4.4 + - + -
106C VAL* 2.8 31.4 + - + +
192C LEU* 4.0 11.2 - - + -
201C TYR* 5.2 2.0 - - - -
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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 GLN 2.9 20.0 + - - +
100C ARG* 3.8 1.8 - - + +
102C PHE* 1.3 74.7 - - - +
104C LEU* 1.3 89.3 + - + +
107C LYS* 3.1 41.9 + - + +
128C TYR 5.2 0.2 - - - -
129C ALA* 3.9 31.6 - - + -
132C ALA* 4.7 5.4 - - + -
188C MET* 3.6 44.9 - - + -
191C TYR* 3.5 40.1 - + + -
192C LEU* 3.8 17.1 - - + +
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Residues in contact with LEU 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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12C MET* 3.4 46.1 - - + +
13C ASP* 3.8 25.1 - - + +
100C ARG* 2.9 31.9 + - + +
101C LEU* 5.0 0.4 - - + -
103C PHE* 1.3 92.5 - - + +
105C GLN* 1.3 54.1 + - - +
107C LYS* 3.3 30.0 + - - +
108C GLU* 2.7 37.1 + - - +
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Residues in contact with GLN 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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12C MET* 3.5 20.3 - - + +
81C ARG* 3.2 23.3 - - - +
82C ALA* 2.8 56.2 + - - +
85C PHE* 4.0 18.6 - - + -
101C LEU 3.4 17.7 + - - +
102C PHE* 3.0 5.0 + - + +
104C LEU* 1.3 77.7 - - - +
106C VAL* 1.3 64.0 + - + +
108C GLU* 3.7 5.2 - - - +
109C ALA* 3.0 25.4 + - + +
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Residues in contact with VAL 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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85C PHE* 3.9 29.2 - - + -
102C PHE* 2.8 27.7 + - + +
103C PHE 4.3 0.7 - - - +
105C GLN* 1.3 71.0 - - + +
107C LYS* 1.3 52.2 + - - +
109C ALA* 3.2 7.6 + - - +
110C ILE* 2.8 48.1 + - + +
115C ILE* 4.7 6.6 - - + +
191C TYR* 4.4 2.9 - - + -
192C LEU* 4.0 16.2 - - + -
195C ALA* 3.7 29.4 - - + -
201C TYR* 3.9 19.5 - - + -
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Residues in contact with LYS 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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103C PHE* 3.1 37.8 + - + +
104C LEU* 3.6 30.4 - - - +
106C VAL* 1.3 76.6 - - - +
108C GLU* 1.3 71.1 + - - +
110C ILE* 3.1 1.5 + - - +
111C LEU* 2.9 50.2 + - + +
129C ALA* 4.2 17.1 - - + +
151C ARG 5.6 3.8 - - - +
191C TYR* 3.1 31.2 - - + +
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Residues in contact with GLU 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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12C MET* 3.7 28.5 - - + +
81C ARG* 4.8 7.1 + - - -
104C LEU 2.7 21.2 + - - +
105C GLN* 3.7 7.2 - - - +
107C LYS* 1.3 75.6 - - - +
109C ALA* 1.3 60.3 + - - +
111C LEU* 3.5 12.3 - - + +
112C ASN* 3.0 52.2 + - - +
114C GLU* 3.9 8.1 - - - +
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Residues in contact with ALA 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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105C GLN* 3.0 19.3 + - + +
106C VAL* 3.4 6.7 - - - +
108C GLU* 1.3 82.1 + - - +
110C ILE* 1.3 64.2 + - - +
112C ASN 3.4 0.7 + - - -
113C ASP 3.2 3.5 + - - -
114C GLU* 3.0 53.0 + - + +
115C ILE* 3.5 15.8 + - + -
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Residues in contact with ILE 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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106C VAL* 2.8 39.3 + - + +
107C LYS 3.1 5.1 + - - +
109C ALA* 1.3 70.8 - - - +
111C LEU* 1.3 67.3 + - + +
113C ASP* 3.2 14.0 + - - -
115C ILE* 3.8 27.4 - - + +
117C CYS* 4.0 23.9 + - + -
122C ALA* 5.5 1.1 - - + -
125C LEU* 3.5 30.5 - - + -
154C PRO* 3.6 19.1 - - + +
191C TYR* 3.8 13.7 - - - +
195C ALA* 4.1 4.3 - - + -
198C LEU* 3.9 14.8 - - + -
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Residues in contact with LEU 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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107C LYS* 2.9 48.6 + - + +
108C GLU* 3.5 9.6 - - + +
110C ILE* 1.3 80.8 - - + +
112C ASN* 1.3 60.1 + - - +
113C ASP* 2.9 14.1 + - - +
151C ARG* 3.4 65.9 + - + +
152C LEU 4.3 21.8 - - - +
153C LEU* 4.4 6.7 - - - +
154C PRO* 3.5 10.8 - - + +
155C GLN* 3.5 5.9 + - - -
191C TYR* 5.0 1.1 - - - +
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Residues in contact with ASN 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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108C GLU* 3.0 44.7 + - - +
109C ALA 3.4 1.7 + - - +
111C LEU* 1.3 72.3 - - - +
113C ASP* 1.3 64.6 + - - +
114C GLU* 3.1 31.5 + - + +
151C ARG* 3.4 17.2 + - - -
155C GLN* 3.7 13.3 + - - +
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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