Contacts of the helix formed by residues 258 - 268 (chain B) in PDB entry 3UGV
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 258 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85B TYR* 5.2 0.2 - - - -
89B ARG* 5.1 4.3 - - - -
102B MET* 4.8 5.4 - - - -
256B PHE* 3.4 3.8 + - - +
257B TYR* 1.3 75.2 - - - +
259B PRO* 1.3 78.3 - - - +
260B ARG* 3.3 3.4 - - - -
261B GLU* 3.2 12.9 + - - +
262B MET 3.4 6.9 + - - -
280B ARG 3.1 9.9 + - - -
281B ILE* 3.6 22.2 - - - +
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Residues in contact with PRO 259 (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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85B TYR* 4.6 6.7 - - - +
89B ARG* 6.1 0.4 - - - +
258B GLY* 1.3 85.7 - - - +
260B ARG* 1.3 58.7 + - - +
262B MET* 2.9 22.1 + - + +
263B HIS* 2.9 14.5 + - - +
281B ILE* 3.7 12.5 - - + +
286B GLY* 3.6 24.0 - - - +
289B ARG* 3.7 22.9 - - + -
290B ALA* 4.1 23.3 - - + +
293B VAL* 4.7 11.0 - - + +
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Residues in contact with ARG 260 (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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258B GLY* 3.3 1.8 - - - -
259B PRO* 1.3 80.0 - - - +
261B GLU* 1.3 57.6 + - - +
263B HIS* 3.1 17.1 + - + +
264B GLN* 3.0 50.2 + - + +
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Residues in contact with GLU 261 (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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98B ALA* 4.6 8.1 - - - +
233B TYR* 5.2 4.6 - - - -
236B PHE* 4.5 11.7 - - + -
255B ASN 3.4 11.8 - - - +
256B PHE* 3.6 12.5 - - + -
257B TYR* 2.7 49.5 + - - +
258B GLY 3.2 11.6 + - - +
260B ARG* 1.3 77.2 - - - +
262B MET* 1.3 63.3 + - - +
264B GLN* 3.3 17.3 + - - +
265B ALA* 3.0 23.7 + - - +
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Residues in contact with MET 262 (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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256B PHE* 3.5 33.7 - - + -
258B GLY 3.4 4.4 + - - +
259B PRO* 2.9 13.1 + - + +
261B GLU* 1.3 80.7 - - - +
263B HIS* 1.3 62.3 + - - +
265B ALA* 3.3 2.1 + - - +
266B LEU* 3.0 37.4 + - + +
274B VAL* 3.9 19.1 - - + -
276B PRO* 3.4 32.8 - - + -
281B ILE* 4.7 1.8 - - + -
290B ALA* 3.8 33.9 - - + +
293B VAL* 4.2 10.5 - - + -
294B ALA* 4.3 11.0 - - - -
301B MET* 4.4 2.7 - - + -
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Residues in contact with HIS 263 (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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259B PRO 2.9 11.9 + - - +
260B ARG* 3.1 22.6 + - + +
262B MET* 1.3 77.6 - - - +
264B GLN* 1.3 65.0 + - + +
266B LEU* 3.5 4.5 + - - +
267B GLN* 3.0 68.5 + - + +
293B VAL* 4.2 23.3 - - + +
297B TRP* 5.0 9.4 + + - +
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Residues in contact with GLN 264 (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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236B PHE* 4.3 10.7 - - + -
260B ARG* 3.0 40.2 + - - +
261B GLU* 3.6 17.9 - - - +
263B HIS* 1.3 84.2 - - + +
265B ALA* 1.3 65.0 + - - +
267B GLN* 3.3 14.8 + - - +
268B ALA* 3.0 22.5 + - - +
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Residues in contact with ALA 265 (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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236B PHE* 3.7 25.0 - - + -
252B ILE* 4.4 8.1 - - + -
256B PHE* 3.5 35.4 - - + -
261B GLU 3.0 12.0 + - - +
262B MET 3.3 1.8 + - - +
264B GLN* 1.3 75.2 - - - +
266B LEU* 1.3 58.5 - - + +
268B ALA* 3.0 16.1 + - - +
269B GLY 3.2 8.7 + - - -
270B ALA* 3.2 14.7 + - + +
271B CYS* 5.0 3.4 - - - -
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Residues in contact with LEU 266 (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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262B MET* 3.0 32.0 + - + +
263B HIS* 3.8 2.7 - - - +
265B ALA* 1.3 72.3 - - + +
267B GLN* 1.3 65.4 + - - +
268B ALA 3.0 1.3 - - - -
269B GLY* 3.0 14.7 + - - +
270B ALA 4.9 1.3 - - - +
271B CYS* 4.0 27.4 - - - +
274B VAL* 4.5 6.3 - - + -
293B VAL* 4.0 15.7 - - + +
294B ALA* 5.0 1.8 - - - -
297B TRP* 3.3 62.6 - - + +
299B ILE* 3.9 26.9 - - + -
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Residues in contact with GLN 267 (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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263B HIS* 3.0 56.7 + - + +
264B GLN* 3.6 15.7 - - - +
266B LEU* 1.3 76.5 - - - +
268B ALA* 1.3 59.6 + - - +
269B GLY 3.2 0.7 + - - -
297B TRP* 3.9 14.6 - - + -
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Residues in contact with ALA 268 (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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236B PHE* 4.3 26.7 - - + +
240B ALA* 3.7 15.1 - - - +
264B GLN 3.0 12.5 + - - +
265B ALA 3.4 10.3 - - - +
266B LEU 3.0 1.2 - - - -
267B GLN* 1.3 77.1 - - - +
269B GLY* 1.3 62.7 + - - +
270B ALA* 4.6 2.0 - - + +
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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
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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