Contacts of the helix formed by residues 118 - 138 (chain B) in PDB entry 2CVP
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 VAL 118 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B LEU* 4.5 1.1 - - + -
102B ALA* 3.9 28.5 - - + -
111B ILE* 2.8 29.0 + - + +
113B VAL* 3.6 31.2 - - + -
116B LYS 3.8 8.1 - - - +
117B ASP* 1.3 71.9 + - - +
119B MET* 1.3 70.3 + - - +
120B PRO 3.4 0.9 - - - -
121B GLU* 3.3 10.1 + - - +
122B VAL* 3.1 21.2 + - + +
269B TRP* 3.7 28.6 - - + +
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Residues in contact with MET 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA* 3.4 39.7 - - - +
105B ASN* 3.4 44.9 - - - +
108B ASN* 3.7 22.2 - - + +
109B THR 3.7 8.7 - - - +
111B ILE* 4.3 3.8 - - - +
117B ASP* 3.1 18.7 + - - +
118B VAL* 1.3 80.0 - - + +
120B PRO* 1.3 65.1 - - + +
122B VAL* 3.7 16.3 - - + +
123B ASN* 2.9 48.2 + - - +
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Residues in contact with PRO 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B ASP* 3.5 30.5 - - + +
118B VAL 3.6 0.4 - - - -
119B MET* 1.3 95.3 - - + +
121B GLU* 1.3 60.5 + - + +
123B ASN* 3.4 6.3 + - + +
124B ARG* 2.9 28.3 + - - +
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Residues in contact with GLU 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B LYS* 6.0 6.7 - - - +
117B ASP 5.3 0.6 + - - +
118B VAL* 3.3 10.0 + - - +
120B PRO* 1.3 79.8 - - + +
122B VAL* 1.3 67.5 + - - +
124B ARG* 2.7 52.5 + - - +
125B VAL* 3.1 29.3 + - - +
267B TRP* 3.8 25.0 + - + +
269B TRP* 6.4 0.4 - - + -
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Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B ALA 3.9 17.7 - - - +
103B LEU* 3.8 31.4 - - + +
118B VAL* 3.1 16.7 + - + +
119B MET* 3.7 19.7 - - + +
121B GLU* 1.3 75.8 - - - +
123B ASN* 1.3 57.4 + - - +
125B VAL* 3.4 2.6 + - - +
126B LEU* 3.0 38.6 + - + +
267B TRP* 3.7 14.8 - - + -
269B TRP* 3.7 28.5 - - + -
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Residues in contact with ASN 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B ARG* 5.2 3.1 + - - -
108B ASN* 2.9 34.7 + - - +
119B MET* 2.9 33.4 + - - +
120B PRO* 3.9 5.3 - - + +
122B VAL* 1.3 74.3 - - - +
124B ARG* 1.3 59.5 + - - +
126B LEU* 3.5 19.9 + - - +
127B ASP* 3.0 39.9 + - - +
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Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PRO 2.9 17.4 + - - +
121B GLU* 2.7 44.1 + - - +
122B VAL 3.3 0.2 - - - -
123B ASN* 1.3 76.1 - - - +
125B VAL* 1.3 76.1 + - - +
127B ASP* 3.3 8.9 + - - +
128B LYS* 3.0 47.4 + - + +
265B GLU* 2.8 31.1 + - - +
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Residues in contact with VAL 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B GLU 3.1 17.4 + - - +
122B VAL 3.9 3.8 - - - +
124B ARG* 1.3 90.8 - - - +
126B LEU* 1.3 67.0 + - + +
128B LYS* 3.2 11.0 + - + +
129B MET* 2.9 31.4 + - + +
264B PHE* 4.6 5.6 - - + -
265B GLU* 3.5 40.4 - - + +
267B TRP* 3.8 14.8 - - + -
279B ALA* 4.0 19.7 - - + +
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Residues in contact with LEU 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B LEU 4.2 8.5 - - - +
106B ARG* 3.9 21.8 - - - +
122B VAL* 3.0 30.3 + - + +
123B ASN* 3.7 24.7 - - - +
124B ARG 3.3 0.2 - - - -
125B VAL* 1.3 76.3 - - - +
127B ASP* 1.3 58.5 + - - +
129B MET* 3.2 14.7 + - - +
130B LYS 2.9 24.6 + - - -
277B TRP 4.8 6.3 - - - +
278B SER 5.8 0.9 - - - -
290B PHE* 3.4 25.1 - - + -
293B PHE* 4.0 26.9 - - + -
297B LEU* 4.1 8.7 - - + -
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Residues in contact with ASP 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B ASN* 3.0 27.0 + - - +
124B ARG* 3.5 8.6 - - - +
125B VAL 3.2 0.2 - - - -
126B LEU* 1.3 76.3 - - - +
128B LYS* 1.3 58.4 + - - +
130B LYS* 3.3 13.8 + - - +
131B SER* 3.0 28.8 + - - -
290B PHE* 6.0 0.7 - - - -
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Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG* 3.0 40.5 + - + +
125B VAL* 3.3 14.6 - - + +
127B ASP* 1.3 74.8 - - - +
129B MET* 1.3 56.8 + - - +
131B SER* 3.3 7.4 + - - -
132B PHE* 2.9 29.6 + - - +
260B PRO 5.7 0.2 - - - -
261B GLN* 2.8 36.1 + - - +
263B MET 3.7 19.1 - - - -
264B PHE* 3.8 19.7 - - + +
265B GLU* 5.7 1.8 - - - +
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Residues in contact with MET 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B VAL* 2.9 27.5 + - + +
126B LEU* 3.4 25.8 - - - +
128B LYS* 1.3 71.6 - - - +
130B LYS* 1.3 58.1 + - - +
132B PHE* 3.3 1.9 + - - +
133B CYS* 2.9 34.4 + - - -
264B PHE* 3.9 22.2 - - + -
278B SER 3.5 19.5 - - - +
279B ALA* 3.8 20.4 - - - -
281B GLY 4.0 0.9 - - - +
282B LEU* 3.7 37.9 - - + +
285B ALA* 4.9 2.5 - - + -
290B PHE* 3.9 8.3 - - + -
293B PHE* 3.9 20.0 - - + -
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Residues in contact with LYS 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B LEU 2.9 13.8 + - - +
127B ASP* 3.3 16.6 + - - +
129B MET* 1.3 75.1 - - - +
131B SER* 1.3 61.9 + - - +
133B CYS* 3.4 3.2 + - - +
134B GLN* 3.1 22.3 + - - +
290B PHE* 3.6 44.4 - - + +
291B ASP* 5.4 7.1 + - - -
294B GLU* 5.2 7.2 + - - +
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Residues in contact with SER 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B ASP 3.0 13.4 + - - -
128B LYS* 3.5 10.8 - - - -
129B MET 3.3 0.2 - - - -
130B LYS* 1.3 73.0 - - - +
132B PHE* 1.3 65.7 + - - +
134B GLN* 3.3 9.3 + - - +
135B ARG* 3.1 28.2 + - - +
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Residues in contact with PHE 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B LYS 2.9 15.9 + - - +
129B MET 3.6 3.6 - - - +
131B SER* 1.3 75.3 + - - +
133B CYS* 1.3 62.1 + - - +
135B ARG* 3.2 6.2 + - - +
136B VAL* 3.0 42.3 + - + +
141B TRP* 3.3 43.1 - + - -
205B LEU* 4.0 13.9 - - + -
244B VAL* 3.8 24.9 - - + -
262B ASN* 4.6 4.0 - - - -
264B PHE* 3.6 20.2 - + + -
282B LEU* 3.8 34.8 - - + -
286B LEU* 3.8 17.5 - - + -
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Residues in contact with CYS 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B MET 2.9 22.0 + - - +
130B LYS* 3.6 7.6 - - - +
131B SER 3.3 0.2 - - - -
132B PHE* 1.3 75.3 - - - +
134B GLN* 1.3 56.9 + - - +
137B ARG* 2.9 48.2 + - - +
282B LEU* 4.2 5.6 - - - -
285B ALA* 3.5 46.0 - - - +
286B LEU* 3.6 20.6 - - - -
290B PHE* 4.6 10.8 - - + +
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Residues in contact with GLN 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B LYS 3.1 13.3 + - - +
131B SER* 3.3 10.6 + - - +
133B CYS* 1.3 75.9 - - - +
135B ARG* 1.3 79.0 + - - +
137B ARG* 5.0 1.8 - - - -
138B SER* 2.8 56.8 + - - +
140B ASP* 3.8 10.3 + - - +
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Residues in contact with ARG 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B SER* 3.1 20.0 + - - +
132B PHE* 3.2 9.8 + - - +
134B GLN* 1.3 89.7 - - - +
136B VAL* 1.3 63.7 + - - +
138B SER* 3.3 3.4 + - - -
140B ASP* 3.1 40.6 + - - +
141B TRP* 2.9 63.1 + - + +
142B LYS 5.1 0.2 - - - +
703B GOL 2.8 34.4 + - - -
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Residues in contact with VAL 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B PHE* 3.0 47.7 + - + +
135B ARG* 1.3 75.0 - - - +
137B ARG* 1.3 66.2 - - - +
139B GLY* 3.1 14.4 + - - -
141B TRP* 4.0 19.0 + - + +
149B ILE* 4.0 40.1 + - + +
152B ILE* 4.1 9.2 - - + -
179B PRO* 4.8 8.5 - - + -
205B LEU* 4.9 3.4 - - + -
286B LEU* 3.7 20.2 - - + -
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Residues in contact with ARG 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B CYS* 2.9 31.0 + - - +
134B GLN* 4.5 1.6 - - - +
136B VAL* 1.3 73.3 - - - +
138B SER* 1.3 59.6 + - - +
139B GLY* 3.2 1.4 + - - -
174B TYR 5.6 0.4 + - - -
176B LYS 4.0 16.0 + - - -
177B GLY* 4.4 17.4 - - - +
178B GLY* 3.3 15.1 - - - +
179B PRO* 4.2 13.0 - - + -
285B ALA 4.0 4.3 - - - -
286B LEU* 3.0 36.5 + - + +
287B HIS 3.2 18.0 + - - -
288B VAL 3.8 4.4 + - - -
289B GLY* 3.3 31.3 - - - +
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Residues in contact with SER 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B GLN* 2.8 37.3 + - - -
135B ARG 3.3 1.4 + - - -
137B ARG* 1.3 77.1 - - - +
139B GLY* 1.3 57.8 + - - +
140B ASP* 3.1 34.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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