Contacts of the helix formed by residues 310 - 322 (chain E) in PDB entry 1UW9
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 HIS 310 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134E ARG* 3.4 39.1 - - - +
135E LEU 2.9 11.0 + - - +
136E GLU* 3.8 15.7 - - - +
302E ASP* 4.2 0.2 - - - -
309E ILE* 1.3 78.1 - - - +
311E PHE* 1.3 74.7 + - + +
312E ARG* 3.0 72.1 + - - +
313E VAL 3.0 12.8 + - - -
314E LEU* 3.5 6.1 + - - +
341E VAL* 3.4 23.3 - - + +
345E PHE* 4.1 9.0 - + - -
473E ASP* 3.0 22.6 + - - -
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Residues in contact with PHE 311 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269E TYR* 4.1 17.5 - - - -
295E ARG* 3.4 34.5 - - + +
298E HIS* 3.9 6.3 - - + -
302E ASP* 3.3 32.1 + - - +
310E HIS* 1.3 83.9 + - + +
312E ARG* 1.3 57.5 + - - +
314E LEU* 3.0 13.6 + - + -
315E ALA* 2.8 36.7 + - + -
326E LEU* 3.8 17.0 - - + -
327E HIS 3.4 22.9 - - - -
328E SER* 4.6 0.4 - - - -
345E PHE* 3.6 42.4 - + + -
349E MET* 4.8 1.3 - - - -
473E ASP* 5.8 1.3 - - - +
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Residues in contact with ARG 312 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136E GLU* 2.8 63.9 + - - +
137E ASP* 4.0 18.2 - - - +
310E HIS* 3.0 43.0 + - - +
311E PHE* 1.3 75.8 - - - +
313E VAL* 1.3 60.0 + - - +
315E ALA* 3.4 2.6 + - - +
316E LYS* 3.0 33.3 + - - +
341E VAL* 4.4 5.9 + - - +
345E PHE* 3.7 30.4 - - + +
348E LEU* 4.1 15.8 - - + +
360E ARG 4.4 3.2 + - - -
361E GLY* 2.8 45.0 + - - -
362E ILE* 5.5 0.4 - - - +
363E TYR* 3.9 4.0 - - - -
475E LEU* 4.1 11.9 - - - +
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Residues in contact with VAL 313 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 4.1 11.9 - - + -
135E LEU* 3.8 23.6 - - + +
136E GLU 3.6 10.5 - - - +
137E ASP* 3.5 39.3 - - - +
138E LEU* 3.8 19.5 - - + +
309E ILE* 3.6 16.8 - - + -
310E HIS 3.0 9.5 + - - +
312E ARG* 1.3 73.7 - - - +
314E LEU* 1.3 61.9 + - - +
315E ALA 3.1 0.2 - - - -
316E LYS* 3.3 7.6 + - - +
317E ALA* 2.9 28.9 + - - +
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Residues in contact with LEU 314 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E PHE* 3.9 26.7 - - + -
269E TYR* 2.9 28.5 + - - +
270E LEU* 4.4 16.6 - - + -
274E PHE* 5.4 0.2 - - + -
298E HIS* 4.1 17.9 - - + +
301E ILE* 4.1 26.5 - - + -
302E ASP* 4.0 24.7 - - + +
309E ILE* 4.0 16.2 - - + +
310E HIS 3.5 8.5 + - - +
311E PHE* 3.0 11.7 + - + +
313E VAL* 1.3 76.7 - - - +
315E ALA* 1.3 57.1 + - - +
317E ALA* 3.6 5.4 + - - +
318E LEU* 3.1 20.1 + - - +
297K MET* 5.8 0.7 - - + -
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Residues in contact with ALA 315 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311E PHE* 2.8 26.0 + - + +
312E ARG* 3.6 9.0 - - - +
314E LEU* 1.3 74.7 - - - +
316E LYS* 1.3 60.6 + - - +
318E LEU* 3.2 3.3 + - - +
319E ARG* 2.9 29.2 + - - +
326E LEU* 3.8 27.1 - - + +
345E PHE* 4.9 4.0 - - + +
348E LEU* 6.1 2.7 - - + -
349E MET* 3.9 21.9 - - + +
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Residues in contact with LYS 316 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137E ASP* 3.2 22.1 + - - +
138E LEU* 2.6 35.4 + - + +
139E ARG* 4.6 0.8 - - - +
140E ILE* 4.4 8.7 - - + -
312E ARG 3.0 20.2 + - - +
313E VAL* 3.3 7.6 + - + +
315E ALA* 1.3 75.9 - - - +
317E ALA* 1.3 61.4 + - - +
319E ARG* 3.2 3.9 + - - +
320E MET* 3.0 34.2 + - - +
348E LEU* 3.8 35.8 - - + +
364E PHE* 4.8 3.4 + - - +
366E GLN* 2.8 32.8 + - - +
368E TRP* 3.7 25.6 - - + -
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Residues in contact with ALA 317 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E VAL* 3.5 11.8 - - + +
116E MET* 4.9 3.5 - - + +
117E PHE* 3.7 28.3 - - + -
274E PHE* 3.7 18.6 - - + -
313E VAL 2.9 16.3 + - - +
314E LEU 3.7 5.2 - - - +
316E LYS* 1.3 76.4 - - - +
318E LEU* 1.3 59.0 + - - +
320E MET* 3.3 10.0 + - - -
321E SER* 2.8 30.3 + - - -
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Residues in contact with LEU 318 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E TYR* 3.6 30.9 - - + -
277E ASN* 3.6 20.4 - - - +
293E ILE* 3.7 30.5 - - + -
314E LEU 3.1 18.0 + - - +
315E ALA 3.2 4.9 + - - +
317E ALA* 1.3 75.0 - - - +
319E ARG* 1.3 58.2 + - - +
321E SER* 4.4 2.9 - - - +
322E GLY* 2.7 38.1 + - - +
323E GLY* 4.1 11.2 - - - +
326E LEU* 3.9 31.9 - - + -
374E VAL* 4.3 9.9 - - + -
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Residues in contact with ARG 319 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151E HYP 2.8 38.7 + - - +
315E ALA 2.9 13.6 + - - +
316E LYS* 3.5 9.0 - - - +
318E LEU* 1.3 77.3 - - - +
320E MET* 1.3 60.1 + - - +
322E GLY 3.7 0.5 + - - -
348E LEU 2.8 34.2 + - - -
349E MET* 3.1 27.6 + - + +
350E ARG 3.9 0.6 + - - -
351E ASP 2.8 31.9 + - - -
352E ASP* 4.6 1.0 - - - +
368E TRP* 3.1 32.6 - - + +
371E MET* 2.8 37.5 + - - +
372E PRO 2.9 19.2 + - - +
373E GLY* 3.6 4.9 - - - +
374E VAL* 3.7 17.7 - - + -
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Residues in contact with MET 320 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E VAL* 3.7 7.9 - - + -
116E MET* 3.9 28.3 - - + -
140E ILE* 3.7 41.7 - - + -
144E TYR* 4.0 1.1 - - + -
145E VAL* 5.7 0.9 - - + -
148E PHE* 3.5 54.3 - - + +
149E VAL 5.0 0.2 + - - -
150E GLY* 3.6 15.1 + - - -
278E THR* 5.6 0.3 - - - +
316E LYS 3.0 20.5 + - - +
317E ALA* 3.6 5.4 - - - +
319E ARG* 1.3 76.1 - - - +
321E SER* 1.3 66.2 + - - +
322E GLY 3.5 0.2 + - - -
368E TRP* 3.8 17.3 - - + -
371E MET* 4.1 12.8 - - + -
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Residues in contact with SER 321 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E VAL* 3.7 8.4 - - - +
148E PHE* 5.0 0.7 - - - -
149E VAL* 6.1 0.3 - - - +
150E GLY 4.2 3.9 + - - +
274E PHE* 3.8 21.0 + - - -
277E ASN* 3.0 19.8 + - - +
278E THR* 2.8 42.1 + - - +
281E ALA* 3.6 14.0 - - - +
317E ALA 2.8 20.0 + - - -
318E LEU* 3.9 3.8 - - - -
320E MET* 1.3 74.8 - - - +
322E GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 322 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150E GLY 3.5 24.7 - - - -
151E HYP 3.8 1.8 - - - -
152E PRO* 4.1 0.7 - - - -
277E ASN* 3.0 18.7 - - - +
281E ALA* 3.8 15.6 - - - +
291E LEU* 3.8 5.7 - - - +
293E ILE* 3.9 0.7 - - - +
318E LEU* 2.7 21.5 + - - +
320E MET 3.3 1.2 - - - -
321E SER* 1.3 75.4 - - - +
323E GLY* 1.3 56.5 + - - -
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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