Contacts of the helix formed by residues 252 - 263 (chain A) in PDB entry 3GNI
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 LYS 252 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207A TYR* 5.1 7.4 - - + +
248A LYS* 3.7 27.0 - - - +
249A TYR* 3.5 1.0 + - - -
250A ILE 3.5 1.0 - - - -
251A SER* 1.3 93.9 + - - +
253A PRO* 1.3 71.8 - - + +
254A GLU* 3.4 23.8 - - - +
255A ASN* 3.3 33.3 + - - +
256A LEU 3.5 7.1 + - - -
281A PHE* 4.2 1.0 - - - -
291A ILE* 3.7 6.8 - - - +
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Residues in contact with PRO 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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251A SER 3.5 8.5 - - - +
252A LYS* 1.3 85.8 - - + +
254A GLU* 1.3 68.3 + - - +
256A LEU* 3.2 5.5 + - - +
257A LYS* 3.0 27.5 + - - +
290A PRO* 3.8 31.0 - - + -
291A ILE* 4.0 10.7 - - + -
294A ILE* 3.8 21.8 - - + +
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Residues in contact with GLU 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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215A GLU* 5.0 15.2 - - - +
252A LYS* 3.4 25.9 - - - +
253A PRO* 1.3 89.8 - - - +
255A ASN* 1.3 66.9 + - - +
257A LYS* 3.6 14.6 - - + +
258A LEU* 3.3 24.4 + - - +
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Residues in contact with ASN 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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207A TYR* 4.6 1.4 + - - -
215A GLU* 5.1 9.0 - - - +
249A TYR* 2.8 57.4 + - + +
252A LYS* 3.3 25.7 + - - +
253A PRO 3.2 0.6 - - - -
254A GLU* 1.3 82.5 + - - +
256A LEU* 1.3 61.2 + - - +
258A LEU* 3.5 7.7 + - - +
259A MET* 3.1 34.0 + - - +
281A PHE* 3.7 16.2 - - + -
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Residues in contact with LEU 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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252A LYS 3.5 0.8 + - - -
253A PRO 3.2 8.6 + - - +
255A ASN* 1.3 74.8 - - - +
257A LYS* 1.3 64.7 + - - +
259A MET* 3.3 1.9 + - + -
260A MET* 2.9 38.0 + - - +
278A PHE* 3.9 27.6 - - + -
281A PHE* 3.5 41.8 - - + -
291A ILE* 3.7 32.8 - - + +
294A ILE* 3.7 28.9 - - + -
295A LEU* 4.0 14.4 - - + -
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Residues in contact with LYS 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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253A PRO 3.0 14.2 + - - +
254A GLU* 3.6 16.6 - - + +
255A ASN 3.3 0.2 - - - -
256A LEU* 1.3 75.8 - - - +
258A LEU* 1.3 58.4 + - - +
260A MET* 3.3 3.1 + - - +
261A ASN* 3.0 45.1 + - - +
294A ILE* 5.0 2.2 - - + +
431B PHE* 3.5 52.6 - - + -
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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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215A GLU* 5.1 11.4 - - + +
218A LEU* 3.6 29.4 - - + +
219A HIS* 3.3 41.3 - - + +
249A TYR* 4.6 4.0 - - - +
254A GLU 3.3 14.9 + - - +
255A ASN* 3.7 6.1 - - - +
256A LEU 3.3 0.2 - - - -
257A LYS* 1.3 79.2 - - - +
259A MET* 1.3 80.0 + - + +
261A ASN* 3.3 11.0 + - + +
262A LEU* 2.9 46.9 + - + +
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Residues in contact with MET 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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218A LEU* 4.0 1.3 - - + -
230A LEU* 3.9 22.7 - - + -
233A LEU* 3.8 15.9 - - + -
249A TYR* 3.5 23.6 - - - +
255A ASN 3.1 15.8 + - - +
256A LEU* 3.8 5.4 - - - +
258A LEU* 1.3 99.3 - - + +
260A MET* 1.3 61.9 + - - +
262A LEU* 3.3 7.0 + - + +
263A LEU* 3.0 27.1 + - - +
274A ALA* 3.9 9.5 - - - +
277A VAL* 3.8 33.4 - - + -
278A PHE* 4.4 18.6 - - + -
281A PHE* 4.1 8.3 - - + -
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Residues in contact with MET 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 LEU* 2.9 28.3 + - - +
257A LYS 3.5 4.3 - - - +
259A MET* 1.3 75.5 - - - +
261A ASN* 1.3 61.2 + - - +
263A LEU* 3.2 23.7 - - + +
264A ARG 3.8 1.0 + - - -
278A PHE* 3.7 24.7 - - + -
294A ILE* 3.7 23.8 - - + -
295A LEU* 4.7 3.4 - - - -
298A ASN* 4.1 17.7 - - + +
302A LEU* 4.0 17.3 - - + -
429B TRP* 2.8 56.5 + - + +
431B PHE* 3.9 14.8 - - + -
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Residues in contact with ASN 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 LYS* 3.0 39.2 + - - +
258A LEU* 3.5 12.4 - - + +
260A MET* 1.3 71.3 - - - +
262A LEU* 1.3 61.0 + - + +
263A LEU 3.1 2.0 - - - -
264A ARG* 2.9 24.4 + - - +
265A ASP* 3.5 6.9 + - - -
428B ASP* 4.8 8.1 - - - +
429B TRP* 3.9 10.2 - - - +
431B PHE* 3.7 16.2 - - - -
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Residues in contact with LEU 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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218A LEU* 4.3 11.9 - - + +
226A LYS* 4.0 31.4 - - + +
230A LEU* 3.8 29.2 - - + -
258A LEU* 2.9 45.3 + - + +
259A MET* 3.3 8.0 + - + +
261A ASN* 1.3 73.1 - - + +
263A LEU* 1.3 59.6 + - - +
264A ARG 3.1 1.1 + - - -
265A ASP* 3.4 23.0 + - - +
270A ILE* 4.0 16.9 - - + +
271A GLN* 3.4 13.2 + - - -
274A ALA* 3.7 16.8 - - + -
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Residues in contact with LEU 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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259A MET 3.0 13.6 + - - +
260A MET* 3.2 25.4 - - - +
261A ASN 3.1 0.4 - - - -
262A LEU* 1.3 75.9 - - - +
264A ARG* 1.3 58.2 + - + +
265A ASP 3.5 0.7 - - - -
271A GLN* 3.4 40.7 + - - +
274A ALA* 4.4 1.3 - - + -
275A PHE* 3.8 24.7 - - + +
278A PHE* 4.1 30.7 - - + -
302A LEU* 5.2 0.7 - - + -
305A PHE* 3.3 37.2 - - + -
306A LEU* 6.0 1.3 - - + -
309A PHE* 4.0 16.1 - - + -
429B TRP* 4.6 8.3 - - + -
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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