Contacts of the helix formed by residues 299 - 310 (chain A) in PDB entry 2H3W
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 VAL 299 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A VAL* 4.2 5.2 - - + -
296A SER* 3.3 32.1 - - - +
298A ASP* 1.3 96.7 + - - +
300A TYR* 1.3 65.3 + - - +
301A ARG 3.4 2.5 - - - -
302A ASN* 3.2 16.8 + - + +
303A HIS* 2.9 51.1 + - + +
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Residues in contact with TYR 300 (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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126A LYS* 2.9 24.9 + - + -
294A ARG* 6.2 3.1 - - - -
295A VAL* 3.9 20.9 - - + +
296A SER 3.1 16.2 + - - +
297A ASP* 3.9 14.8 + - - +
298A ASP 3.6 1.0 - - - -
299A VAL* 1.3 77.0 - - - +
301A ARG* 1.3 69.3 + - + +
303A HIS* 3.1 5.7 + - + +
304A VAL* 3.0 45.3 + - + +
334A ASP* 2.5 29.4 + - - -
336A SER* 2.9 14.2 + - - -
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Residues in contact with ARG 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.7 36.2 + - + +
297A ASP 5.0 1.4 + - - -
298A ASP 5.5 0.4 - - - -
299A VAL 3.4 0.4 - - - -
300A TYR* 1.3 87.0 - - + +
302A ASN* 1.3 58.0 + - - +
304A VAL* 3.3 6.7 + - + +
305A ALA* 3.0 27.4 + - - +
411A MET* 3.6 34.3 - - + +
412A LEU 5.5 0.4 - - - +
413A THR* 4.1 21.3 + - - -
561A ASP 5.4 4.8 + - - -
562A CYS 5.6 0.2 - - - -
563A VAL* 3.8 17.0 - - - +
586A ASN* 5.0 10.5 - - - +
587A PHE 5.7 0.4 + - - -
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Residues in contact with ASN 302 (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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298A ASP 4.0 17.4 + - - -
299A VAL* 3.2 15.1 + - + +
300A TYR 3.2 0.8 - - - -
301A ARG* 1.3 75.2 - - - +
303A HIS* 1.3 62.1 + - + +
305A ALA* 3.4 4.1 + - - +
306A GLY* 3.1 22.9 + - - -
409A ILE* 3.5 32.1 + - + +
410A MET* 3.5 19.5 - - - +
411A MET* 2.7 39.1 + - - +
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Residues in contact with HIS 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A VAL* 3.9 30.3 - - + +
299A VAL* 2.9 44.8 + - + +
300A TYR* 3.5 9.2 - - + +
302A ASN* 1.3 79.1 - - + +
304A VAL* 1.3 60.2 + - + +
306A GLY* 3.4 2.1 + - - +
307A GLN* 3.0 27.4 + - - +
312A GLY* 6.0 0.5 - - - -
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Residues in contact with VAL 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 4.1 16.6 - - + -
300A TYR* 3.0 48.8 + - + +
301A ARG* 3.7 8.5 - - + +
303A HIS* 1.3 75.5 - - + +
305A ALA* 1.3 65.9 + - - +
307A GLN* 3.3 13.4 + - - +
308A MET* 3.1 34.4 + - + +
334A ASP* 5.3 0.4 - - - +
336A SER* 3.9 26.0 - - - +
337A CYS 5.4 1.6 - - - +
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123A ILE* 3.4 22.4 - - + +
301A ARG 3.0 11.0 + - - +
302A ASN 3.5 9.4 - - - +
304A VAL* 1.3 78.0 - - - +
306A GLY* 1.3 57.7 + - - +
308A MET 3.3 0.7 + - - -
309A LEU* 2.9 25.2 + - - +
409A ILE* 4.3 10.5 - - + -
411A MET* 3.7 21.1 - - + -
565A PHE* 3.1 24.3 - - + -
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Residues in contact with GLY 306 (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 ASN 3.1 14.5 + - - -
303A HIS* 3.8 4.0 - - - -
304A VAL 3.2 0.2 - - - -
305A ALA* 1.3 74.9 - - - +
307A GLN* 1.3 59.2 + - - +
309A LEU* 4.4 0.9 - - - -
310A HIS* 2.8 59.3 + - - -
311A GLY 3.0 4.9 + - - -
312A GLY* 4.3 1.3 - - - -
409A ILE* 4.3 7.8 - - - +
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Residues in contact with GLN 307 (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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289A ASP* 3.0 36.1 - - - +
290A LYS 5.0 1.2 - - - +
292A VAL* 4.6 18.8 - - + +
303A HIS 3.0 13.4 + - - +
304A VAL* 3.4 24.1 - - - +
305A ALA 3.3 0.2 - - - -
306A GLY* 1.3 77.6 - - - +
308A MET* 1.3 70.9 + - + +
311A GLY* 3.1 27.9 + - - +
312A GLY* 4.1 2.6 - - - +
317A ASN* 3.8 9.4 + - - +
321A ARG* 2.9 25.2 + - - +
330A ILE* 4.7 0.5 - - - +
332A ALA* 3.8 18.7 - - - +
334A ASP* 5.4 1.8 + - - -
336A SER* 5.2 0.8 - - - -
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Residues in contact with MET 308 (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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121A GLY* 4.4 0.2 - - - -
122A VAL 3.9 16.2 - - - +
123A ILE* 4.1 9.0 - - + -
304A VAL* 3.1 29.9 + - + +
305A ALA 3.7 3.8 - - - +
307A GLN* 1.3 88.2 - - - +
309A LEU* 1.3 61.5 + - - +
321A ARG* 5.0 1.0 + - - -
330A ILE* 3.6 40.4 - - + +
332A ALA* 4.8 0.4 - - + -
336A SER* 4.2 6.1 - - - +
337A CYS* 3.5 34.8 - - - +
338A GLY* 3.7 9.2 - - - +
339A MET 4.0 4.9 - - - +
340A VAL* 3.3 30.1 - - - +
565A PHE* 3.8 13.5 - - + -
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Residues in contact with LEU 309 (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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115A VAL* 3.9 6.8 - - - +
116A ILE* 4.1 27.2 + - + -
119A SER* 3.4 25.3 - - - +
121A GLY* 3.8 16.6 - - - +
305A ALA 2.9 17.3 + - - +
306A GLY* 3.9 2.2 - - - +
308A MET* 1.3 79.6 - - - +
310A HIS* 1.3 60.0 + - - +
323A PHE* 3.9 14.6 - - - -
340A VAL* 4.2 5.8 - - - +
407A LEU* 3.6 30.5 - - + -
409A ILE* 4.3 9.2 - - + -
565A PHE* 3.8 19.0 - - + +
566A PHE* 4.6 6.1 - - - +
567A GLY 4.6 8.5 - - - +
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Residues in contact with HIS 310 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A VAL* 3.6 23.3 - - + -
116A ILE* 3.7 18.5 - - + +
306A GLY* 2.8 36.0 + - - -
309A LEU* 1.3 75.6 - - - +
311A GLY* 1.3 54.1 + - - +
312A GLY* 2.9 33.2 + - - -
318A SER* 2.6 28.4 + - - -
321A ARG* 5.0 0.4 - - - -
323A PHE* 3.7 15.2 - - - -
400A LEU* 4.4 5.0 - - + +
404A ILE* 3.5 42.3 - - + +
407A LEU* 3.9 20.6 - - + +
409A ILE* 4.7 1.8 - - + -
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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
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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