Contacts of the helix formed by residues 331 - 337 (chain W) in PDB entry 3EXG
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 PRO 331 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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308V LEU* 4.5 2.0 - - - +
113W LYS* 4.3 16.4 - - + -
118W LYS* 6.2 0.7 - - + -
329W GLU 3.4 4.2 - - - +
330W PRO* 1.3 91.7 - - + +
332W LEU* 1.3 66.4 + - - +
333W GLU* 4.1 20.0 - - + +
334W GLU* 2.9 48.3 + - + +
335W LEU 4.0 1.7 + - - -
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Residues in contact with LEU 332 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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307V ILE* 4.3 17.5 - - + +
308V LEU* 4.2 16.4 - - + -
311V ASN* 3.2 48.9 - - + +
330W PRO 3.4 4.2 + - - -
331W PRO* 1.3 71.6 - - - +
333W GLU* 1.3 68.2 + - - +
335W LEU* 3.2 19.6 + - + +
357W PHE* 3.5 21.8 - - + -
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Residues in contact with GLU 333 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331W PRO* 4.1 15.3 - - + +
332W LEU* 1.3 86.5 + - - +
334W GLU* 1.3 66.3 + - + +
335W LEU 3.3 0.9 + - - -
336W GLY 4.1 4.3 + - - -
337W TYR* 4.0 18.2 + - - +
357W PHE* 4.5 11.7 - - - -
358W LYS* 4.4 6.2 + - - +
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Residues in contact with GLU 334 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308V LEU* 5.2 0.7 - - - -
118W LYS* 3.8 25.6 - - - +
120W LYS* 3.4 17.3 + - - +
330W PRO* 5.5 3.9 - - + +
331W PRO* 2.9 35.8 + - + +
333W GLU* 1.3 79.7 - - + +
335W LEU* 1.3 63.1 + - - +
336W GLY 3.0 4.3 + - - -
337W TYR* 3.0 51.5 + - + +
338W HIS* 5.2 3.1 + - - -
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Residues in contact with LEU 335 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298V ALA* 4.5 13.5 - - + -
300V VAL* 4.2 10.4 - - + +
303V PRO* 4.4 2.9 - - + -
308V LEU* 3.1 54.1 - - + +
311V ASN* 4.2 11.4 - - + +
312V SER* 3.5 11.4 - - - +
120W LYS* 4.0 5.3 - - - +
331W PRO 4.0 1.4 + - - -
332W LEU* 3.2 17.9 + - + +
333W GLU 3.3 0.4 - - - -
334W GLU* 1.3 76.0 - - - +
336W GLY* 1.3 60.6 + - - +
357W PHE* 3.4 41.3 - - + -
102X TYR* 3.0 30.7 + - - +
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Residues in contact with GLY 336 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300V VAL* 4.7 3.8 - - - -
333W GLU 4.1 4.6 + - - -
334W GLU 3.1 1.4 - - - -
335W LEU* 1.3 82.7 - - - +
337W TYR* 1.3 65.4 + - - +
339W ILE* 3.3 13.5 - - - +
348W VAL* 4.4 8.5 - - - -
357W PHE* 4.4 13.6 - - - +
358W LYS 3.6 17.9 + - - -
359W SER* 3.1 17.8 + - - -
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Residues in contact with TYR 337 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120W LYS* 3.4 12.0 + - - +
333W GLU* 4.0 15.0 + - - +
334W GLU* 3.0 58.0 + - + +
336W GLY* 1.3 80.9 - - - +
338W HIS* 1.3 91.1 + + + +
358W LYS* 3.3 39.8 + - + +
360W VAL* 3.5 37.4 - - + +
102X TYR* 3.8 6.4 - - - -
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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