Contacts of the helix formed by residues 331 - 337 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3082 LEU* 3.9 7.8 - - - +
113Y LYS* 4.3 19.3 - - + -
329Y GLU 3.5 3.8 - - - +
330Y PRO* 1.3 91.6 - - + +
332Y LEU* 1.3 65.0 + - - +
333Y GLU* 3.2 18.7 + - - +
334Y GLU* 3.3 45.9 + - + +
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Residues in contact with LEU 332 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3072 ILE* 4.5 20.1 - - + +
3082 LEU* 4.1 11.2 - - + -
3112 ASN* 3.3 43.1 - - + +
330Y PRO 3.9 1.2 + - - -
331Y PRO* 1.3 74.7 - - - +
333Y GLU* 1.3 66.5 + - + +
334Y GLU 3.1 1.2 + - - -
335Y LEU* 3.2 21.2 + - + +
357Y PHE* 4.3 19.6 - - + -
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Residues in contact with GLU 333 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331Y PRO* 3.9 20.2 - - + +
332Y LEU* 1.3 85.3 + - + +
334Y GLU* 1.3 65.8 + - + +
335Y LEU 3.2 3.7 + - - -
336Y GLY 4.4 1.0 + - - -
337Y TYR* 3.9 17.0 - - - +
357Y PHE* 4.9 10.1 - - + -
358Y LYS* 4.3 11.1 + - - +
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Residues in contact with GLU 334 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3082 LEU* 4.6 2.0 - - - -
118Y LYS* 5.6 7.1 - - - +
120Y LYS* 3.5 12.7 - - - -
330Y PRO* 5.4 4.8 - - + +
331Y PRO* 3.3 38.9 + - + +
332Y LEU 3.1 1.4 + - - -
333Y GLU* 1.3 83.1 - - + +
335Y LEU* 1.3 64.9 + - - +
336Y GLY 3.1 2.5 - - - -
337Y TYR* 3.1 59.2 + - + +
338Y HIS* 5.7 1.4 + - - -
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Residues in contact with LEU 335 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2982 ALA* 4.3 15.0 - - + -
3002 VAL* 4.3 9.1 - - + +
3032 PRO* 3.6 16.8 - - + -
3082 LEU* 3.3 33.5 - - + +
3112 ASN* 4.3 6.3 - - + +
3122 SER* 3.3 22.9 - - - +
120Y LYS* 3.9 2.4 - - - +
332Y LEU* 3.2 17.9 + - + +
333Y GLU 3.2 1.0 - - - -
334Y GLU* 1.3 78.3 - - - +
336Y GLY* 1.3 58.3 + - - +
357Y PHE* 3.3 44.4 - - + -
102Z TYR* 3.0 26.2 + - - +
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Residues in contact with GLY 336 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3002 VAL* 4.5 8.7 - - - -
333Y GLU 4.4 0.2 + - - -
334Y GLU* 3.1 1.6 - - - +
335Y LEU* 1.3 80.0 - - - +
337Y TYR* 1.3 57.4 + - - +
339Y ILE* 3.5 9.9 - - - +
348Y VAL* 4.3 13.0 - - - -
357Y PHE* 4.3 9.9 - - - +
358Y LYS 3.7 18.1 + - - -
359Y SER* 2.8 28.2 + - - -
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Residues in contact with TYR 337 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120Y LYS* 3.0 16.7 + - - +
333Y GLU* 3.9 12.9 + - - +
334Y GLU* 3.1 54.1 + - + +
335Y LEU 3.4 0.8 - - - -
336Y GLY* 1.3 77.3 - - - +
338Y HIS* 1.3 96.2 + + + +
358Y LYS* 3.6 29.8 - - + +
360Y VAL* 3.8 45.2 - - + +
102Z TYR* 3.4 6.6 - - - -
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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