Contacts of the helix formed by residues 314 - 326 (chain A) in PDB entry 4B7B
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 SER 314 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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291A SER* 3.9 32.2 + - - -
294A THR* 4.1 5.2 - - - +
311A TYR 3.4 2.6 - - - +
312A ARG 3.3 0.6 - - - -
313A GLU* 1.3 80.1 - - - +
315A LYS* 1.3 64.7 + - - +
316A LEU* 3.7 7.0 + - - +
317A THR* 3.2 33.3 + - - +
318A ARG* 3.2 27.0 + - - -
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Residues in contact with LYS 315 (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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163A ILE* 4.3 7.0 - - + -
166A GLU* 3.3 44.1 + - + +
168A LEU* 4.1 28.3 - - + -
181A ARG* 4.3 14.1 - - - +
184A MET* 4.1 17.9 - - - +
314A SER* 1.3 71.2 - - - +
316A LEU* 1.3 61.8 + - - +
318A ARG* 3.2 14.2 + - - +
319A ILE* 2.9 37.5 + - + +
1387A CO 4.2 9.3 + - - +
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Residues in contact with LEU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A PHE* 4.4 2.0 - - + -
163A ILE* 3.8 26.0 - - + +
236A HIS* 4.1 22.7 - - + +
238A VAL* 4.0 16.8 - - + -
264A VAL* 4.2 9.6 - - + -
266A LEU* 3.6 25.8 - - + -
291A SER* 5.0 6.0 - - - +
292A LEU* 5.6 0.7 - - + -
295A LEU* 4.3 22.9 - - + -
314A SER* 3.8 7.8 - - - +
315A LYS* 1.3 80.0 - - - +
317A THR* 1.3 57.3 + - + +
319A ILE* 3.6 3.8 + - + +
320A LEU* 3.1 55.7 + - + +
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Residues in contact with THR 317 (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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294A THR* 3.9 1.1 - - + +
295A LEU* 4.0 33.2 - - + +
298A VAL* 3.8 22.7 - - + -
310A PRO 3.8 2.1 + - - -
311A TYR* 2.4 46.0 + - - +
314A SER* 3.2 22.2 + - - +
316A LEU* 1.3 77.4 - - + +
318A ARG* 1.3 60.9 + - - +
320A LEU* 3.6 4.7 - - + -
321A GLN* 2.9 29.6 + - - +
324A LEU* 5.0 2.9 - - + +
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Residues in contact with ARG 318 (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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184A MET* 3.4 46.1 + - + +
186A ASP* 3.4 20.6 + - - +
192A ARG 4.5 4.0 - - - +
193A GLY 5.4 0.2 - - - -
194A VAL* 4.2 16.9 - - + +
311A TYR* 3.7 9.6 - - + +
312A ARG* 3.3 52.5 - - + +
314A SER 3.2 21.7 + - - +
315A LYS* 3.5 13.2 - - - +
317A THR* 1.3 75.2 + - - +
319A ILE* 1.3 65.9 + - - +
321A GLN* 3.2 21.5 + - - +
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Residues in contact with ILE 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A LEU* 4.5 15.0 - - + -
163A ILE* 4.0 19.5 - - + -
168A LEU* 4.3 21.8 - - + -
184A MET* 3.3 22.2 - - + -
194A VAL* 4.3 9.3 - - - +
196A ILE* 4.2 17.7 - - + -
238A VAL* 4.9 12.6 - - + -
315A LYS* 2.9 26.9 + - + +
316A LEU* 3.8 3.6 - - - +
318A ARG* 1.3 77.6 - - - +
320A LEU* 1.3 75.3 + - + +
321A GLN 3.7 0.3 + - - -
322A ASP* 4.6 7.3 + - - +
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Residues in contact with LEU 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 4.5 13.2 - - + +
102A PHE* 3.7 27.4 - - + -
238A VAL* 4.4 10.5 - - + -
262A ASN* 4.2 26.5 - - + +
264A VAL* 4.2 5.6 - - + -
295A LEU* 5.6 0.4 - - + -
316A LEU* 3.1 42.2 + - + +
317A THR* 3.6 1.3 - - - +
318A ARG 3.1 0.4 - - - -
319A ILE* 1.3 96.4 - - + +
321A GLN* 1.3 64.5 + - - +
322A ASP 3.2 2.9 - - - -
323A SER* 3.1 15.1 + - - +
324A LEU* 3.1 26.1 + - + +
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Residues in contact with GLN 321 (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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191A LYS 4.6 4.7 + - - +
192A ARG* 3.6 43.2 - - + +
311A TYR* 3.3 56.0 - - + +
312A ARG* 5.2 11.8 + - - +
317A THR 2.9 19.9 + - - +
318A ARG* 3.2 11.9 + - - +
320A LEU* 1.3 73.3 - - - +
322A ASP* 1.3 64.3 + - - +
325A GLY* 2.9 23.5 + - - -
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Residues in contact with ASP 322 (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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98A ASN* 4.3 15.7 - - - +
190A ASN* 3.4 27.2 + - - -
192A ARG* 3.7 16.1 + - - +
193A GLY* 4.1 9.1 - - - -
318A ARG 4.8 0.2 + - - -
319A ILE 4.6 6.9 + - - +
320A LEU 3.1 1.5 + - - -
321A GLN* 1.3 79.8 - - - +
323A SER* 1.3 64.4 + - - +
325A GLY* 3.8 3.3 + - - -
326A GLY* 3.8 9.5 + - - -
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Residues in contact with SER 323 (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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98A ASN* 3.0 35.0 + - - +
99A CYS 4.4 0.4 - - - -
100A THR* 3.2 23.8 - - - -
260A LYS* 5.4 0.7 - - - +
262A ASN* 2.6 24.5 + - - -
319A ILE 5.7 0.2 + - - -
320A LEU* 3.1 9.8 + - - -
322A ASP* 1.3 80.2 - - - +
324A LEU* 1.3 63.5 + - - +
325A GLY 3.2 0.7 + - - -
326A GLY* 3.7 2.8 + - - -
328A THR* 3.2 23.7 + - - -
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Residues in contact with LEU 324 (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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100A THR* 4.3 9.0 - - - +
102A PHE* 4.1 20.0 - - + -
295A LEU* 4.6 8.1 - - + -
298A VAL* 4.2 20.2 - - + -
299A ILE* 4.3 8.7 - - + -
302A LEU* 3.8 26.5 - - + +
311A TYR* 4.0 13.7 - - + -
317A THR* 5.0 4.5 - - - +
320A LEU* 3.1 33.9 + - + +
323A SER* 1.3 75.4 - - - +
325A GLY* 1.3 60.2 + - - +
326A GLY 3.5 1.1 + - - +
328A THR* 3.9 14.3 - - - +
330A THR* 3.7 33.0 + - + +
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Residues in contact with GLY 325 (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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302A LEU* 5.4 2.0 - - - -
311A TYR* 3.5 18.4 - - - -
321A GLN* 2.9 17.9 + - - -
322A ASP 4.5 0.4 - - - -
323A SER 3.2 0.2 + - - -
324A LEU* 1.3 77.3 - - - +
326A GLY* 1.3 61.2 + - - +
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Residues in contact with GLY 326 (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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322A ASP 3.8 8.3 + - - -
323A SER 3.7 5.2 + - - -
324A LEU 3.5 1.9 - - - +
325A GLY* 1.3 81.8 - - - +
327A ARG* 1.3 64.7 + - - -
328A THR* 3.3 13.7 + - - +
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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