Contacts of the helix formed by residues 257 - 267 (chain A) in PDB entry 3UGM
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 THR 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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217A LEU 6.0 6.1 - - - -
220A ALA* 5.3 10.1 - - + -
248A LEU* 5.0 10.5 - - + +
249A ARG* 5.6 4.3 + - - -
256A ASP* 1.4 81.8 + - - +
258A GLY* 1.3 58.1 + - - +
259A GLN 2.5 4.3 + - - -
260A LEU* 2.2 41.9 + - + +
261A VAL* 3.1 9.7 + - + -
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Residues in contact with GLY 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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220A ALA* 6.0 1.6 - - - -
224A ASP* 4.9 5.8 - - - -
256A ASP* 5.7 0.2 - - - -
257A THR* 1.3 78.4 - - - +
259A GLN* 1.3 51.7 + - - +
260A LEU 3.4 0.2 - - - -
261A VAL* 3.4 21.1 - - - +
262A LYS* 2.8 30.0 + - - +
265A LYS* 5.2 0.9 + - - -
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Residues in contact with GLN 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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255A LEU* 3.8 9.9 - - + +
256A ASP* 3.3 51.3 + - + +
257A THR 2.5 3.3 + - - +
258A GLY* 1.3 71.7 - - - +
260A LEU* 1.3 50.7 + - - +
262A LYS* 2.6 32.8 + - - +
263A ILE* 2.8 21.0 + - + +
291A PRO* 4.3 11.1 + - - +
292A ALA* 5.5 1.8 - - - +
295A VAL* 3.2 41.8 - - + +
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Residues in contact with LEU 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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241A LEU* 3.4 28.0 - - + +
244A ASP* 3.1 32.1 - - + +
245A ALA* 5.7 5.4 - - + -
248A LEU* 4.5 12.1 - - + -
255A LEU* 3.4 32.8 - - + -
256A ASP 2.8 28.9 - - - +
257A THR* 2.2 23.6 + - + +
259A GLN* 1.3 72.4 - - - +
261A VAL* 1.3 59.7 + - + +
263A ILE* 3.1 21.2 + - + +
264A ALA 3.0 18.4 + - - -
272A MET* 5.1 4.3 - - + -
275A VAL* 6.2 0.7 - - + -
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Residues in contact with VAL 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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220A ALA* 4.7 11.2 - - + -
224A ASP* 3.6 44.2 - - + +
225A ILE* 4.8 5.4 - - + +
228A VAL* 4.4 9.6 - - + -
241A LEU* 4.7 13.2 - - + -
257A THR* 3.1 8.0 + - + +
258A GLY* 3.4 22.7 - - - +
260A LEU* 1.3 76.7 - - + +
262A LYS* 1.3 58.3 + - - +
264A ALA* 3.3 6.1 + - - +
265A LYS* 2.8 36.6 + - + +
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Residues in contact with LYS 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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258A GLY 2.8 13.7 + - - +
259A GLN* 2.6 19.5 + - - +
261A VAL* 1.3 69.4 - - - +
263A ILE* 1.3 64.1 + - - +
264A ALA 3.2 0.2 + - - -
265A LYS* 3.2 30.0 + - - +
266A ARG* 3.3 17.9 + - - +
292A ALA 5.6 1.2 + - - -
295A VAL* 3.6 29.7 + - + +
296A ALA* 4.6 8.0 - - - +
299A SER* 3.2 32.4 - - - +
25C G 3.7 32.4 + - - +
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Residues in contact with ILE 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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255A LEU* 4.3 11.2 - - + -
259A GLN* 2.8 22.8 + - + +
260A LEU* 3.1 33.6 + - + +
262A LYS* 1.3 76.1 - - - +
264A ALA* 1.3 58.1 + - - +
267A GLY* 2.9 30.3 + - - -
268A GLY 3.5 2.9 + - - +
271A ALA* 4.7 5.3 - - + +
272A MET* 5.0 11.4 - - - -
275A VAL* 4.5 14.4 - - + -
294A VAL* 6.1 0.9 - - + -
295A VAL* 3.5 37.0 - - + -
298A ALA* 3.8 30.3 - - + -
299A SER* 4.6 6.1 - - - +
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Residues in contact with ALA 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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228A VAL* 3.7 22.8 - - + +
231A GLN* 5.0 1.4 - - - +
237A ALA* 4.3 10.3 - - + +
241A LEU* 4.2 9.0 - - + -
260A LEU 3.0 14.5 + - - +
261A VAL* 3.8 4.7 - - - +
263A ILE* 1.3 78.2 - - - +
265A LYS* 1.3 65.1 + - - +
268A GLY* 3.6 17.2 + - - +
272A MET* 3.6 31.0 - - + -
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Residues in contact with LYS 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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224A ASP* 5.2 3.4 - - - +
227A GLY* 3.7 27.6 - - - +
228A VAL* 3.2 13.2 - - + +
231A GLN* 3.4 27.6 - - - +
258A GLY 5.2 0.6 + - - -
261A VAL* 2.8 28.3 + - + +
262A LYS* 3.2 30.6 + - - +
264A ALA* 1.3 76.5 - - - +
266A ARG* 1.3 67.3 + - + +
268A GLY* 4.6 1.2 + - - -
26C A 3.6 35.9 + - - +
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Residues in contact with ARG 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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232A TRP* 5.3 3.3 + - - -
262A LYS* 3.3 13.2 + - - +
265A LYS* 1.3 93.5 - - + +
267A GLY* 1.3 59.2 + - - +
268A GLY 3.4 2.0 - - - -
299A SER* 3.3 40.3 + - - +
300A ASN* 2.7 39.0 + - - +
301A ASN* 3.8 12.0 + - - +
335A ASP* 3.6 21.0 + - - -
25C G 4.5 15.1 - - - +
26C A 3.4 50.5 + - - +
27C T 3.8 20.9 + - - +
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Residues in contact with GLY 267 (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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232A TRP* 4.5 3.4 - - - -
262A LYS 4.1 0.2 + - - -
263A ILE 2.9 16.8 + - - -
266A ARG* 1.3 79.9 - - - +
268A GLY* 1.3 66.1 + - - +
270A THR* 3.4 11.1 - - - +
271A ALA* 3.4 17.5 + - - +
298A ALA 3.3 17.1 + - - -
299A SER 4.2 0.6 - - - -
300A ASN 3.2 14.3 - - - +
301A ASN* 5.1 1.7 - - - +
0B T 4.9 0.2 + - - -
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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