Contacts of the helix formed by residues 310 - 322 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134H ARG* 3.4 38.8 - - - +
135H LEU 2.9 11.2 + - - +
136H GLU* 3.8 15.3 - - - +
302H ASP* 4.3 0.2 - - - -
309H ILE* 1.3 83.5 - - - +
311H PHE* 1.3 81.6 + - + +
312H ARG* 3.0 63.8 + - - +
313H VAL* 3.1 12.1 + - - +
314H LEU* 3.5 2.3 + - - +
341H VAL* 3.4 23.0 - - + +
345H PHE* 4.1 8.7 - + - -
473H ASP* 2.9 23.4 + - - -
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Residues in contact with PHE 311 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H TYR* 4.1 17.0 - - - -
295H ARG* 3.5 33.7 - - + -
298H HIS* 3.9 5.8 - - + -
302H ASP* 3.3 32.5 + - - +
310H HIS* 1.3 80.0 + - + +
312H ARG* 1.3 56.0 + - - +
314H LEU* 2.9 13.9 + - + -
315H ALA* 2.8 38.1 + - + -
326H LEU* 3.8 17.3 - - + -
327H HIS 3.4 22.0 - - - -
328H SER* 4.7 0.7 - - - -
345H PHE* 3.7 37.0 - + - -
349H MET* 4.7 1.3 - - - -
1482H EDO 3.5 15.5 - - - -
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Residues in contact with ARG 312 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136H GLU* 2.8 66.1 + - - +
137H ASP* 4.0 17.5 - - - +
310H HIS* 3.0 43.6 + - + +
311H PHE* 1.3 77.4 - - - +
313H VAL* 1.3 59.8 + - - +
315H ALA* 3.4 3.5 + - - +
316H LYS* 3.0 32.9 + - - +
341H VAL* 4.4 5.7 + - - +
344H GLY 6.2 0.4 - - - -
345H PHE* 3.7 29.8 - - + +
348H LEU* 4.1 15.4 - - + +
360H ARG 4.5 2.8 + - - -
361H GLY* 2.9 45.5 + - - -
362H ILE* 5.5 0.4 - - - +
363H TYR* 4.0 1.8 - - - -
475H LEU* 4.1 11.3 - - - +
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Residues in contact with VAL 313 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE* 4.2 11.9 - - + -
135H LEU* 3.8 19.1 - - + +
136H GLU 3.6 24.0 - - - +
137H ASP* 3.6 24.9 - - - +
138H LEU* 3.8 28.3 - - + +
309H ILE* 3.5 21.5 - - + -
310H HIS 3.1 2.3 + - - +
312H ARG* 1.3 73.9 - - + +
314H LEU* 1.3 60.3 + - - +
315H ALA 3.1 0.4 - - - -
316H LYS* 3.3 8.7 + - + +
317H ALA* 2.9 28.6 + - - +
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Residues in contact with LEU 314 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H PHE* 3.9 25.8 - - + -
269H TYR* 2.9 29.2 + - - +
270H LEU* 4.3 17.5 - - + -
274H PHE* 5.4 0.4 - - + -
298H HIS* 4.0 28.7 - - + +
301H ILE* 4.0 25.6 - - + -
302H ASP* 4.0 15.7 - - + +
309H ILE* 4.0 16.2 - - + -
310H HIS 3.9 8.7 - - - +
311H PHE* 2.9 12.4 + - + +
313H VAL* 1.3 76.2 - - - +
315H ALA* 1.3 56.3 + - - +
317H ALA* 3.6 4.4 + - - +
318H LEU* 3.1 19.6 + - - +
297R MET* 5.9 0.4 - - + -
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Residues in contact with ALA 315 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311H PHE* 2.8 25.7 + - + +
312H ARG* 3.6 8.7 - - - +
314H LEU* 1.3 75.8 - - - +
316H LYS* 1.3 60.2 + - + +
318H LEU* 3.3 2.6 + - - +
319H ARG* 2.9 29.3 + - - +
326H LEU* 3.8 25.8 - - + +
345H PHE* 4.9 4.0 - - + -
348H LEU* 6.1 1.6 - - + -
349H MET* 3.9 21.9 - - + +
374H VAL* 5.8 0.2 - - - +
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Residues in contact with LYS 316 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137H ASP* 3.2 22.7 + - - +
138H LEU* 2.6 34.6 + - + +
139H ARG* 4.6 0.8 - - - +
140H ILE* 4.4 7.6 - - + -
312H ARG 3.0 16.9 + - - +
313H VAL* 3.6 10.5 - - + +
315H ALA* 1.3 72.4 - - - +
317H ALA* 1.3 65.6 + - - +
319H ARG* 3.2 3.6 + - - +
320H MET* 3.0 33.9 + - - +
348H LEU* 3.8 36.4 - - + +
364H PHE* 4.9 3.2 + - - +
366H GLN* 2.8 33.1 + - - +
368H TRP* 3.7 23.5 - - + -
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Residues in contact with ALA 317 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 3.5 11.9 - - + +
116H MET* 4.9 2.7 - - + +
117H PHE* 3.7 22.0 - - + -
274H PHE* 3.7 27.4 - - + -
313H VAL 2.9 17.4 + - - +
314H LEU 3.7 3.4 - - - +
315H ALA 3.3 0.2 - - - -
316H LYS* 1.3 75.1 - - - +
318H LEU* 1.3 58.6 + - - +
320H MET* 3.3 10.8 + - - -
321H SER* 2.8 29.6 + - - -
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Residues in contact with LEU 318 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269H TYR* 3.5 35.8 - - + +
277H ASN* 3.6 11.2 - - - +
293H ILE* 3.7 31.4 - - + -
314H LEU 3.1 12.9 + - - +
315H ALA 3.7 4.3 - - - +
316H LYS 3.3 0.2 - - - -
317H ALA* 1.3 73.4 - - - +
319H ARG* 1.3 59.6 + - - +
321H SER* 4.4 2.5 - - - +
322H GLY* 2.7 47.4 + - - +
323H GLY* 4.0 11.0 - - - +
326H LEU* 3.9 31.9 - - + -
374H VAL* 4.3 8.7 - - + -
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Residues in contact with ARG 319 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151H HYP 2.8 37.9 + - - +
315H ALA 2.9 13.3 + - - +
316H LYS* 3.2 8.9 + - - +
318H LEU* 1.3 76.2 - - - +
320H MET* 1.3 60.2 + - - +
322H GLY 3.7 0.9 + - - -
348H LEU 2.8 35.0 + - - -
349H MET* 3.1 27.5 + - - +
350H ARG 4.0 0.4 + - - -
351H ASP 2.9 31.9 + - - -
352H ASP* 4.6 1.2 - - - +
368H TRP* 3.2 31.5 - - + +
371H MET* 2.8 37.7 + - - +
372H PRO 2.9 19.2 + - - +
373H GLY* 3.6 4.8 - - - -
374H VAL* 3.7 16.8 - - + -
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Residues in contact with MET 320 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 3.7 7.2 - - + -
116H MET* 3.8 28.9 - - + -
140H ILE* 3.8 41.7 - - + -
144H TYR* 4.0 0.9 - - + -
145H VAL* 5.7 0.9 - - + -
148H PHE* 3.4 53.9 - - + +
150H GLY* 3.6 15.1 + - - -
278H THR* 5.6 0.5 - - - +
316H LYS 3.0 23.6 + - - +
317H ALA* 3.5 6.5 - - - +
319H ARG* 1.3 74.4 - - - +
321H SER* 1.3 65.2 + - - +
322H GLY 3.5 0.2 + - - -
368H TRP* 3.8 17.0 - - + -
371H MET* 4.1 13.0 - - + -
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Residues in contact with SER 321 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113H VAL* 3.7 9.1 - - - +
148H PHE* 5.0 0.7 - - - -
149H VAL* 6.1 0.3 - - - +
150H GLY* 4.3 3.0 + - - +
274H PHE* 3.8 18.6 + - - -
277H ASN* 3.0 22.9 + - - +
278H THR* 2.9 42.5 + - - +
281H ALA* 3.6 14.2 - - - +
282H ILE* 6.0 0.2 - - - +
317H ALA 2.8 20.1 + - - -
318H LEU* 4.0 4.3 - - - -
320H MET* 1.3 74.0 - - - +
322H GLY* 1.3 58.4 + - - +
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Residues in contact with GLY 322 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150H GLY 3.6 24.0 - - - -
151H HYP 3.8 1.8 - - - -
152H PRO* 4.1 0.7 - - - -
277H ASN* 3.0 20.3 - - - +
281H ALA* 3.8 10.3 - - - +
291H LEU* 3.8 10.4 - - - +
293H ILE* 4.0 0.3 - - - +
318H LEU* 2.7 21.7 + - - +
320H MET 3.3 1.2 - - - -
321H SER* 1.3 74.1 - - - +
323H GLY* 1.3 56.8 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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