Contacts of the helix formed by residues 335 - 340 (chain A) in PDB entry 2HA7
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 GLY 335 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295A PHE* 5.8 0.2 - - - -
333A ASP 3.1 0.8 - - - -
334A GLU* 1.3 79.3 - - - +
336A SER* 1.3 65.0 + - - +
337A TYR 3.2 2.7 - - - -
338A PHE* 3.1 21.4 + - - +
339A LEU* 3.6 11.5 - - - +
399A SER* 3.5 22.1 + - - -
402A VAL* 4.3 7.7 - - - +
403A GLY* 3.7 15.0 - - - -
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ASP* 3.7 10.2 + - - -
334A GLU 3.7 0.4 - - - -
335A GLY* 1.3 75.9 - - - +
337A TYR* 1.3 65.1 + - - +
339A LEU* 3.3 19.7 + - - +
340A VAL* 4.3 1.7 + - - +
399A SER* 3.5 23.8 + - - -
442A TRP* 4.0 17.0 - - - -
443A MET* 2.8 50.4 + - - +
446A PRO* 4.0 4.2 - - - +
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Residues in contact with TYR 337 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLY 4.3 0.9 + - - -
83A THR* 4.6 3.1 - - - +
86A TRP* 3.7 14.5 - - - -
333A ASP 5.0 0.2 + - - -
336A SER* 1.3 84.3 + - - +
338A PHE* 1.3 81.1 + + + +
339A LEU 3.3 0.9 + - - -
340A VAL* 3.5 21.4 - - - +
341A TYR* 3.7 18.6 + + - -
439A TRP* 3.4 42.4 - + - -
443A MET* 4.5 9.0 - - - -
446A PRO* 4.5 11.7 - - + -
447A HIS* 4.2 26.0 - + + -
449A TYR* 4.4 8.1 - + - -
908A ETM 2.8 30.9 - - - -
909A BUA 5.4 0.4 - - + -
910A BCH 3.4 32.3 - - + -
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Residues in contact with PHE 338 (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 ILE* 3.6 34.0 - - + +
295A PHE* 3.3 49.6 - + + -
297A PHE* 4.5 4.7 - + - -
334A GLU 3.7 18.8 - - - -
335A GLY* 3.1 10.8 + - - +
337A TYR* 1.3 82.8 - + + +
339A LEU* 1.3 63.5 + - - +
340A VAL 3.3 0.2 - - - -
341A TYR* 3.3 16.5 + - - +
402A VAL* 4.3 4.9 - - + -
447A HIS* 3.5 34.8 - + + -
900A IOD 4.0 19.3 - - + -
909A BUA 3.9 23.8 - - + -
910A BCH 4.2 10.3 - - + -
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Residues in contact with LEU 339 (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 ILE* 3.9 7.4 - - + -
335A GLY 3.6 13.0 - - - +
336A SER* 3.6 10.3 - - - +
337A TYR 3.2 0.8 - - - -
338A PHE* 1.3 78.4 - - - +
340A VAL* 1.3 56.9 + - - +
341A TYR 3.1 1.0 + - - -
343A VAL* 3.0 37.9 + - + +
346A PHE* 3.4 47.5 - - + +
398A MET* 4.0 14.4 - - + +
399A SER* 3.6 33.2 - - - +
402A VAL* 3.8 29.2 - - + -
442A TRP* 4.6 4.0 - - + -
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Residues in contact with VAL 340 (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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76A LEU* 3.4 22.9 - - + +
77A TYR* 3.8 19.6 + - + +
336A SER 4.6 1.1 - - - +
337A TYR 3.5 15.3 - - - +
339A LEU* 1.3 76.3 - - - +
341A TYR* 1.3 73.3 + - + +
342A GLY 3.4 3.5 + - - -
343A VAL 5.9 0.2 - - - -
346A PHE 4.1 11.6 - - - +
347A SER* 3.7 28.5 - - - +
348A LYS 3.9 0.2 - - - +
439A TRP* 4.4 9.6 - - + -
442A TRP* 4.1 9.6 - - + -
443A MET* 3.7 25.4 - - + -
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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