Contacts of the helix formed by residues 240 - 253 (chain B) in PDB entry 1V2E
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 PHE 240 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MET* 4.3 24.2 - - + -
2A ARG* 5.3 0.9 - - - -
3A LEU* 4.0 30.3 - - + -
187B PHE* 3.9 25.6 - + - -
212B GLU 4.4 6.5 - - - -
215B PHE* 3.6 25.4 - + + -
237B PRO* 2.9 32.3 + - + +
239B GLU* 1.3 110.8 - - + +
241B MET* 1.3 66.6 + - - +
242B PRO* 3.5 1.8 - - - -
243B ARG* 3.1 24.7 + - - +
244B LEU* 3.3 9.6 + - + +
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Residues in contact with MET 241 (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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79B GLU 3.3 27.6 - - - +
80B SER* 3.6 17.5 - - - +
82B VAL* 3.6 27.7 - - + +
215B PHE* 4.4 3.6 - - - -
234B ILE* 3.5 38.6 - - + +
236B GLY* 3.8 15.0 - - - +
237B PRO 3.6 16.6 - - - +
238B LYS* 3.7 3.1 - - - +
240B PHE* 1.3 73.1 - - - +
242B PRO* 1.3 71.2 - - + +
243B ARG 2.8 6.9 + - - -
244B LEU* 2.8 27.6 + - + +
245B ALA* 3.0 12.5 + - - +
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Residues in contact with PRO 242 (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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10A ALA 4.3 4.5 - - - +
12A GLU 5.8 1.9 + - - -
79B GLU 5.2 0.4 - - - +
238B LYS 3.1 16.6 - - - +
239B GLU 3.9 7.2 - - - +
240B PHE 3.5 3.6 - - - -
241B MET* 1.3 91.3 - - + +
243B ARG* 1.3 64.5 + - + +
245B ALA* 3.9 7.4 + - + +
246B GLY* 3.4 15.6 + - - -
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Residues in contact with ARG 243 (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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3A LEU* 3.2 32.9 - - + +
7A THR* 3.9 28.9 + - + -
8A GLU* 4.8 9.7 + - - +
10A ALA* 3.3 24.5 + - - +
11A LYS* 5.2 4.4 - - - +
239B GLU 4.9 4.0 + - - +
240B PHE* 3.2 14.6 - - - +
241B MET 2.8 1.2 + - - -
242B PRO* 1.3 80.1 - - + +
244B LEU* 1.3 63.5 + - + +
245B ALA 3.1 1.8 - - - -
246B GLY 2.9 15.4 + - - -
247B MET* 2.9 13.4 + - - +
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Residues in contact with LEU 244 (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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3A LEU* 4.9 7.6 - - + -
82B VAL* 4.6 5.5 - - + +
93B VAL* 3.8 11.4 - - + +
94B LEU* 3.5 31.0 - - + -
97B SER* 3.5 32.5 - - - +
98B LEU* 5.5 0.4 - - + -
215B PHE* 4.0 19.3 - - + -
234B ILE* 3.9 24.2 - - + +
240B PHE 3.3 14.3 + - - +
241B MET* 2.8 21.5 + - + +
243B ARG* 1.3 77.8 - - + +
245B ALA* 1.3 61.7 + - - +
247B MET* 3.4 3.9 + - - +
248B ARG* 3.3 23.9 + - - +
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Residues in contact with ALA 245 (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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60B PRO* 4.2 4.7 - - + +
61B ALA* 4.2 24.5 - - + +
82B VAL* 4.1 17.8 - - + +
241B MET 3.0 13.1 + - - +
242B PRO* 4.1 7.6 - - + +
244B LEU* 1.3 76.9 - - - +
246B GLY* 1.3 59.2 + - - +
248B ARG* 3.3 12.7 - - - +
249B GLN* 2.9 30.9 + - - +
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Residues in contact with GLY 246 (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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10A ALA* 3.4 23.1 - - - -
11A LYS 4.5 3.1 - - - -
12A GLU* 5.5 0.9 - - - -
242B PRO 3.4 8.8 + - - -
243B ARG 2.9 8.4 + - - -
245B ALA* 1.3 80.9 - - - +
247B MET* 1.3 57.2 + - - +
249B GLN* 3.3 19.1 - - - +
250B TRP* 3.1 26.3 + - - -
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Residues in contact with MET 247 (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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6A ARG* 4.2 17.3 - - + +
7A THR* 4.1 18.8 - - + -
10A ALA* 3.9 17.5 - - + -
121A LEU* 4.7 16.8 - - + +
93B VAL* 3.4 20.6 - - + -
96B GLN* 3.7 41.7 - - + +
97B SER* 3.4 19.1 - - - +
243B ARG 2.9 17.9 + - - +
244B LEU 3.8 1.3 - - - +
245B ALA 3.2 0.6 - - - -
246B GLY* 1.3 72.9 - - - +
248B ARG* 1.3 58.4 + - - +
249B GLN 3.0 4.0 - - - -
250B TRP* 3.0 26.2 + - - +
251B THR* 3.5 12.5 + - + +
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Residues in contact with ARG 248 (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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60B PRO 3.2 18.5 + - - -
82B VAL* 4.4 7.4 - - + -
83B VAL 3.1 22.0 + - - -
84B THR* 3.4 6.0 - - + +
85B SER* 3.3 17.8 + - - +
89B GLU* 3.2 24.4 + - + +
93B VAL* 3.8 18.5 - - + +
244B LEU 3.3 12.9 + - - +
245B ALA* 3.3 18.4 - - - +
247B MET* 1.3 74.2 - - - +
249B GLN* 1.3 67.0 + - - +
250B TRP 3.1 0.2 - - - -
251B THR* 2.9 23.9 + - - +
252B SER* 3.2 17.0 + - - -
253B PHE 3.1 23.2 + - - -
254B SER* 3.1 7.6 - - - +
255B ALA 3.3 19.2 - - - +
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Residues in contact with GLN 249 (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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11A LYS 3.0 18.6 + - - +
12A GLU* 3.7 13.1 - - - +
13A SER* 3.0 31.6 + - - +
16A PRO* 4.5 0.8 - - - +
88A THR* 3.8 4.0 - - - +
114A VAL* 5.5 0.9 - - - +
60B PRO* 3.8 26.0 - - + +
245B ALA 2.9 19.8 + - - +
246B GLY* 3.3 12.1 - - - +
248B ARG* 1.3 79.0 - - - +
250B TRP* 1.3 88.2 + - + +
253B PHE* 3.0 47.0 + - + +
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Residues in contact with TRP 250 (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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9A ALA* 3.0 30.1 + - - +
10A ALA* 3.9 2.4 - - - +
11A LYS* 3.9 9.4 - - + -
13A SER* 4.7 2.5 - - - -
88A THR* 3.6 9.5 - - - +
92A TYR* 3.4 19.9 - - + +
113A ASP* 3.5 47.6 - - - -
114A VAL* 4.0 16.3 - - + +
117A PRO* 3.7 27.2 - - + +
118A ASP* 3.9 13.5 - - - +
121A LEU* 4.0 27.1 - - + -
246B GLY 3.1 20.2 + - - -
247B MET* 3.0 11.3 + - - +
249B GLN* 1.3 106.3 - - + +
251B THR* 1.3 64.0 + - - +
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Residues in contact with THR 251 (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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88A THR* 3.3 3.9 - - - +
89A GLU* 2.9 35.6 + - - -
92A TYR* 4.1 34.3 - - + -
251A THR* 5.1 9.0 - - + -
89B GLU* 2.6 28.0 + - + +
92B TYR* 4.3 14.6 - - + -
93B VAL* 4.4 7.9 - - + -
247B MET 3.5 10.3 + - - +
248B ARG* 2.9 16.6 + - - -
250B TRP* 1.3 78.4 - - - +
252B SER* 1.3 60.9 + - - +
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Residues in contact with SER 252 (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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85A SER* 3.8 28.7 - - - -
88A THR* 3.9 2.7 - - - -
89A GLU* 4.5 5.6 - - - -
230A ARG* 3.2 12.7 + - - -
85B SER* 2.6 28.7 + - - -
89B GLU* 2.7 18.1 + - - -
248B ARG* 3.2 6.1 + - - -
251B THR* 1.3 80.8 + - - +
253B PHE* 1.3 56.7 + - - +
254B SER 2.5 26.9 + - - +
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Residues in contact with PHE 253 (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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13A SER* 4.8 4.3 - - - -
16A PRO* 4.2 12.3 - - + -
32A GLN* 3.9 10.3 - - - -
88A THR* 3.6 11.2 - - + +
113A ASP* 6.0 1.1 - - - -
114A VAL* 6.0 4.7 - - + -
230A ARG* 3.6 13.2 - - - +
520A KMT 3.7 35.4 - - + -
57B TYR* 3.9 25.4 - + - -
58B ALA 3.6 22.0 - - - -
60B PRO* 3.2 49.5 - - + +
248B ARG* 3.1 12.6 + - - -
249B GLN* 3.0 38.5 + - + +
252B SER* 1.3 73.7 - - - +
254B SER* 1.3 78.4 + - - +
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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