Contacts of the helix formed by residues 248 - 263 (chain A) in PDB entry 1V1A
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 GLY 248 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A ASN* 4.2 0.6 - - - +
246A PRO 3.2 0.8 + - - -
247A VAL* 1.3 77.3 - - - +
249A ALA* 1.3 63.6 + - - +
250A GLY 3.1 3.7 + - - -
251A ASP* 3.3 10.0 + - - +
252A ALA* 3.3 15.8 + - - +
281A VAL* 3.8 9.4 - - - +
287A ASP 3.9 11.9 - - - +
1302A KDG 3.5 28.9 + - - -
1303A ADP 4.4 4.3 + - - -
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Residues in contact with ALA 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A PRO* 2.9 18.6 + - + +
247A VAL 3.0 1.7 + - - -
248A GLY* 1.3 78.1 - - - +
250A GLY* 1.3 58.8 + - - +
252A ALA 3.6 0.2 + - - -
253A PHE* 3.1 19.6 + - - +
278A GLY* 3.4 32.4 - - - +
281A VAL* 4.1 6.3 - - - -
282A ALA* 3.9 10.1 - - + +
1303A ADP 3.5 34.9 + - + +
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Residues in contact with GLY 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ASP* 4.3 3.0 - - - +
165A ASN* 6.1 0.4 - - - -
219A LYS* 3.8 18.0 + - - -
248A GLY* 3.1 1.0 - - - -
249A ALA* 1.3 77.7 - - - +
251A ASP* 1.3 60.9 + - - +
252A ALA 3.2 0.2 - - - -
253A PHE* 3.1 10.3 + - - +
254A ALA* 2.8 29.5 + - - +
1303A ADP 3.1 28.1 + - - -
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Residues in contact with ASP 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA* 3.2 20.6 - - - +
38A ASN* 2.8 40.4 + - + -
39A VAL* 3.6 16.7 - - + +
163A ASP* 4.1 1.3 - - - +
165A ASN* 3.4 20.1 + - - +
248A GLY* 3.3 5.1 + - - +
250A GLY* 1.3 74.1 - - - +
252A ALA* 1.3 65.2 + - - +
254A ALA* 3.5 2.8 + - - -
255A ALA* 3.0 26.2 + - - +
1302A KDG 2.6 31.9 + - - -
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 5.4 1.1 - - - +
42A ALA* 4.8 7.4 - - + -
248A GLY 3.3 4.8 + - - +
249A ALA 3.6 9.2 - - - +
250A GLY 3.2 0.2 - - - -
251A ASP* 1.3 76.6 - - - +
253A PHE* 1.3 69.4 + - - +
255A ALA* 3.4 5.8 + - - +
256A GLY 3.1 15.4 + - - -
277A LEU* 3.2 33.1 - - + +
281A VAL* 3.4 36.6 - - + -
288A HIS* 6.3 0.4 - - + -
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Residues in contact with PHE 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A PHE* 3.8 16.8 - + - -
217A VAL* 3.7 29.2 - - + -
219A LYS* 3.5 29.2 - - + -
225A ALA* 4.2 12.3 - - + -
249A ALA 3.1 15.0 + - - +
250A GLY* 3.1 12.3 + - - +
252A ALA* 1.3 75.5 - - - +
254A ALA* 1.3 66.8 + - - +
256A GLY* 2.9 14.7 + - - -
257A TYR* 3.0 10.2 + + - -
271A LEU* 4.2 6.3 - - + -
274A ALA* 3.1 55.5 - - + +
275A ASN* 3.7 17.7 - - - -
278A GLY 4.1 0.8 - - - +
1303A ADP 4.0 21.8 - - - +
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Residues in contact with ALA 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A VAL* 4.5 3.4 - - + -
130A HIS* 4.5 15.9 - - + -
163A ASP* 4.5 6.7 - - - +
191A PHE* 3.6 38.3 - - + -
250A GLY 2.8 17.8 + - - +
251A ASP* 3.8 7.6 - - - +
253A PHE* 1.3 73.2 - - - +
255A ALA* 1.3 58.2 + - - +
257A TYR* 3.2 2.6 + - - +
258A LEU* 2.9 35.7 + - + +
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Residues in contact with ALA 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 3.6 24.0 - - + +
42A ALA* 3.5 30.5 - - + -
43A LEU* 3.0 21.1 - - + +
46A LEU* 4.9 1.6 - - + -
251A ASP 3.0 18.3 + - - +
252A ALA 3.7 2.5 - - - +
254A ALA* 1.3 76.0 - - - +
256A GLY* 1.3 58.2 + - - +
258A LEU* 4.4 2.0 - - - -
259A ALA* 2.9 23.9 + - - +
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Residues in contact with GLY 256 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A LEU* 4.7 1.3 - - - -
252A ALA 3.1 6.5 + - - -
253A PHE 2.9 7.6 + - - -
255A ALA* 1.3 73.9 - - - +
257A TYR* 1.3 67.7 + - - +
259A ALA* 3.4 4.0 + - - -
260A GLY 3.1 4.9 + - - -
273A LEU* 3.0 33.2 - - - +
274A ALA* 4.0 10.8 - - - -
277A LEU* 3.9 22.6 - - - +
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Residues in contact with TYR 257 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LEU* 3.9 15.5 - - + -
191A PHE* 3.6 30.3 - + + -
215A GLU* 2.9 29.1 + - - -
217A VAL* 3.8 19.8 - - + +
227A ALA* 3.9 5.9 - - - +
253A PHE* 3.0 7.2 + + - +
254A ALA 3.4 7.4 - - - +
256A GLY* 1.3 78.7 - - - +
258A LEU* 1.3 63.0 + - - +
260A GLY* 3.1 1.2 + - - -
261A ALA* 2.9 25.0 + - + +
267A VAL* 3.7 13.6 - - - +
270A ARG* 3.1 53.6 + - + +
271A LEU* 3.8 20.4 - - + -
274A ALA* 3.7 16.2 - - + +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A VAL* 4.8 5.8 - - + -
39A VAL* 4.4 14.6 - - + -
43A LEU* 4.6 12.1 - - + -
128A PHE* 3.5 40.8 - - + -
130A HIS* 4.1 34.3 - - + +
161A SER* 4.0 8.3 - - - +
189A LEU* 4.0 16.4 - - + -
191A PHE* 4.5 3.8 - - + -
254A ALA* 2.9 20.8 + - + +
255A ALA* 3.7 4.9 - - - +
257A TYR* 1.3 77.4 - - - +
259A ALA* 1.3 51.8 + - - +
261A ALA* 3.1 4.7 + - + +
262A VAL* 2.7 44.6 + - + +
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Residues in contact with ALA 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.9 15.0 - - + +
46A LEU* 4.2 11.2 - - + -
48A VAL* 4.1 15.9 - - + -
255A ALA 2.9 18.6 + - - +
256A GLY 3.7 4.5 - - - +
257A TYR 3.3 0.2 - - - -
258A LEU* 1.3 75.6 - - - +
260A GLY* 1.3 54.1 + - - +
262A VAL* 3.2 3.4 + - - +
263A TRP* 2.7 61.7 + - + -
273A LEU* 4.3 1.3 - - + -
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Residues in contact with GLY 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256A GLY 3.1 8.5 + - - -
257A TYR 3.6 2.5 - - - -
259A ALA* 1.3 78.5 - - - +
261A ALA* 1.3 65.8 + - - +
263A TRP* 3.0 15.9 + - - +
264A GLY 3.0 7.6 + - - -
265A LEU* 3.1 18.7 + - - +
270A ARG* 4.0 13.9 - - - -
273A LEU* 3.3 21.1 - - - +
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Residues in contact with ALA 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A ARG* 3.5 7.0 + - - -
128A PHE* 3.9 21.1 - - + -
159A ARG* 5.9 2.0 - - - +
189A LEU* 5.8 1.6 - - + -
257A TYR* 2.9 17.3 + - + +
258A LEU* 3.2 12.3 - - + +
260A GLY* 1.3 74.9 - - - +
262A VAL* 1.3 55.0 + - - +
263A TRP 2.7 0.5 + - - -
264A GLY* 2.4 32.3 + - - -
265A LEU 4.8 0.4 - - - +
270A ARG* 3.8 24.0 - - - +
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Residues in contact with VAL 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 3.9 35.7 - - + +
4A VAL* 3.9 18.4 - - + -
48A VAL* 4.7 4.3 - - + -
127A ARG* 2.6 37.1 + - + +
128A PHE* 3.4 28.9 - - + -
258A LEU* 2.7 25.1 + - - +
259A ALA* 3.5 7.6 - - - +
261A ALA* 1.3 72.2 - - - +
263A TRP* 1.3 65.3 + - + +
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Residues in contact with TRP 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A GLU* 5.4 4.0 + - - -
46A LEU* 3.3 39.0 - - + -
47A GLY 5.2 1.4 - - - -
48A VAL* 3.9 22.8 - - + +
259A ALA* 2.7 32.1 + - + +
260A GLY* 3.3 12.1 - - - +
261A ALA 2.9 0.6 - - - -
262A VAL* 1.3 81.0 - - + +
264A GLY* 1.3 64.0 + - - +
265A LEU* 3.6 20.8 + - + +
273A LEU* 3.9 25.1 - - + -
294A ARG* 4.7 18.2 - - - -
297A LEU* 4.4 13.9 - - + -
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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