Contacts of the helix formed by residues 251 - 266 (chain A) in PDB entry 2VK2
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 MET 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A TRP* 4.0 11.9 - - + -
20A GLU* 3.5 26.2 - - - +
89A LEU* 4.1 14.5 - - + +
90A ASP* 3.9 12.3 - - + -
105A VAL* 3.5 47.3 - - + +
106A THR* 4.0 1.8 - - - -
107A ALA 4.1 7.0 - - - +
247A LEU* 3.4 34.8 - - + -
248A THR* 3.5 13.7 - - + +
249A PRO 2.9 8.2 + - - +
250A ASN* 1.3 73.2 - - - +
252A ALA* 1.3 63.7 + - - +
253A GLY 3.4 0.7 - - - -
254A PRO* 3.5 8.3 - - - +
255A ALA* 3.7 8.1 + - - +
275A THR* 3.8 17.7 - - - +
1298A GZL 4.9 0.2 - - - +
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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
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20A GLU* 5.3 3.0 - - + +
23A VAL 5.0 0.2 - - - -
24A ALA* 3.7 38.6 - - + +
27A GLU* 4.9 1.1 - - + -
63A PHE* 4.2 3.5 - - + -
89A LEU* 3.9 17.4 - - + +
249A PRO 4.7 0.6 + - - -
250A ASN* 3.4 2.3 - - - +
251A MET* 1.3 79.1 - - - +
253A GLY* 1.3 59.3 + - - +
255A ALA* 3.1 5.1 + - - +
256A PHE* 2.8 47.7 + - + -
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Residues in contact with GLY 253 (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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27A GLU* 3.9 11.3 - - - +
31A ARG* 3.3 19.4 + - - -
250A ASN* 2.8 24.7 + - - -
252A ALA* 1.3 72.6 - - - +
254A PRO* 1.3 60.6 - - - +
256A PHE* 3.1 3.6 + - - -
257A ASP* 2.8 33.2 + - - -
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Residues in contact with PRO 254 (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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103A THR* 5.9 0.2 - - - +
105A VAL* 3.9 25.4 - - + -
250A ASN* 3.2 26.9 - - - +
251A MET 3.5 5.4 - - - +
253A GLY* 1.3 89.3 - - - +
255A ALA* 1.3 54.9 + - - +
257A ASP* 3.4 13.1 + - + +
258A ALA* 3.1 28.1 + - - +
273A THR* 4.2 15.4 - - + +
275A THR* 5.2 5.8 - - + -
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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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63A PHE* 3.6 26.0 - - + -
87A PHE* 4.0 14.1 - - + -
89A LEU* 3.9 21.1 - - + -
105A VAL* 4.0 10.9 - - + +
251A MET 3.7 8.2 + - - +
252A ALA 3.1 9.5 + - - +
254A PRO* 1.3 74.9 - - - +
256A PHE* 1.3 60.4 + - - +
258A ALA* 3.3 4.2 + - - +
259A LEU* 2.9 28.9 + - - +
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Residues in contact with PHE 256 (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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5A VAL* 4.0 10.8 - - + -
24A ALA 3.7 19.1 - - - -
27A GLU* 3.8 13.5 - - + -
28A ALA* 3.7 23.6 - - + -
31A ARG* 3.5 28.3 - - - +
33A ILE* 3.6 33.7 - - + -
35A LEU* 4.2 11.7 - - + -
63A PHE* 3.5 27.1 - + - -
252A ALA* 2.8 40.0 + - + -
253A GLY 3.5 2.5 - - - +
255A ALA* 1.3 70.7 - - - +
257A ASP* 1.3 58.6 + - - +
259A LEU* 3.6 5.8 - - + +
260A GLU* 2.9 34.7 + - - +
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Residues in contact with ASP 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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31A ARG* 2.9 28.4 + - - +
253A GLY 2.8 19.2 + - - +
254A PRO* 3.5 16.6 - - + +
255A ALA 3.3 0.2 - - - -
256A PHE* 1.3 76.8 - - - +
258A ALA* 1.3 61.5 + - - +
260A GLU* 3.8 6.0 - - - +
261A LYS* 3.2 33.4 + - + +
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Residues in contact with ALA 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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87A PHE* 3.9 15.0 - - + -
103A THR* 4.9 4.5 - - + -
254A PRO 3.1 13.8 + - - +
255A ALA* 3.7 5.4 - - - +
257A ASP* 1.3 75.8 - - - +
259A LEU* 1.3 60.9 + - - +
261A LYS* 3.4 8.4 + - - +
262A TYR* 3.0 30.1 + - - +
267A THR 4.5 2.1 - - - +
269A PRO* 3.9 29.0 - - + +
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Residues in contact with LEU 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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3A LEU* 4.3 17.3 - - + -
5A VAL* 3.5 32.3 - - + -
33A ILE* 5.2 1.8 - - + -
60A ASP 5.7 0.4 - - - -
61A ALA* 3.6 24.9 - - + -
63A PHE* 4.4 8.3 - - + -
85A PRO* 4.4 2.5 - - + -
87A PHE* 3.7 21.4 - - + -
255A ALA 2.9 17.6 + - - +
256A PHE* 3.6 9.4 - - + +
258A ALA* 1.3 77.2 - - - +
260A GLU* 1.3 57.1 + - - +
262A TYR* 3.2 4.0 + - + +
263A LYS* 2.9 61.3 + - + +
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Residues in contact with GLU 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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3A LEU* 4.8 10.5 - - + -
31A ARG* 3.2 55.4 + - - +
33A ILE* 3.8 13.3 - - + +
256A PHE 2.9 14.4 + - - +
257A ASP* 3.8 7.2 - - - +
259A LEU* 1.3 76.8 - - + +
261A LYS* 1.3 57.6 + - + +
263A LYS* 3.5 4.4 + - - +
264A LYS* 3.0 31.3 + - - +
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Residues in contact with LYS 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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257A ASP* 3.2 20.4 + - + +
258A ALA* 3.7 7.0 - - - +
260A GLU* 1.3 79.3 - - + +
262A TYR* 1.3 62.3 + - - +
264A LYS* 3.4 16.4 + - - +
265A ASP* 2.9 31.3 + - - +
267A THR* 4.2 22.0 - - + +
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Residues in contact with TYR 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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85A PRO* 4.1 28.7 - - + +
87A PHE* 5.2 0.2 - + - -
102A MET* 3.5 29.1 - - + -
258A ALA 3.0 18.2 + - - +
259A LEU* 3.2 7.8 + - + +
261A LYS* 1.3 77.2 - - - +
263A LYS* 1.3 71.2 + - + +
266A GLY* 2.7 46.2 + - - -
267A THR 3.3 21.0 + - - +
268A MET* 3.5 22.6 - - - -
269A PRO* 5.3 0.2 - - + -
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Residues in contact with LYS 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 LEU* 4.1 23.3 - - + -
60A ASP* 2.9 47.0 + - - +
83A GLU 5.3 2.0 + - - -
85A PRO* 4.0 14.3 - - - +
259A LEU* 2.9 43.3 + - + +
260A GLU* 4.1 3.8 - - - +
262A TYR* 1.3 79.8 - - + +
264A LYS* 1.3 63.4 + - - +
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Residues in contact with LYS 264 (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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260A GLU 3.0 17.4 + - - +
261A LYS* 3.7 16.4 - - - +
262A TYR 3.2 0.4 - - - -
263A LYS* 1.3 80.4 - - - +
265A ASP* 1.3 74.8 + - + +
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Residues in contact with ASP 265 (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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261A LYS* 2.9 17.1 + - - +
264A LYS* 1.3 94.0 - - + +
266A GLY* 1.3 63.1 + - - +
267A THR* 2.6 28.8 + - - -
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Residues in contact with GLY 266 (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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262A TYR* 2.7 40.8 + - - -
263A LYS 4.7 0.2 - - - -
265A ASP* 1.3 72.5 - - - +
267A THR* 1.3 63.3 + - - +
268A MET* 3.2 10.6 + - - +
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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