Contacts of the helix formed by residues 331 - 335 (chain 5) 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 5).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3084 LEU* 4.0 8.3 - - - +
1135 LYS* 4.6 17.7 - - + -
3295 GLU 3.5 3.5 - - - +
3305 PRO* 1.3 90.3 - - + +
3325 LEU* 1.3 63.1 + - - +
3335 GLU* 3.4 23.3 - - + +
3345 GLU* 3.1 46.8 + - + +
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Residues in contact with LEU 332 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3074 ILE* 4.3 21.5 - - + +
3084 LEU* 4.1 17.7 - - + -
3114 ASN* 3.4 52.3 - - + +
3305 PRO 3.7 2.0 + - - -
3315 PRO* 1.3 71.7 - - - +
3335 GLU* 1.3 64.8 + - - +
3345 GLU 3.3 2.9 + - - -
3355 LEU* 3.4 16.8 - - + +
3575 PHE* 3.7 20.4 - - + -
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Residues in contact with GLU 333 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3331 GLU* 5.7 1.4 - - - +
3315 PRO* 3.4 16.4 - - + +
3325 LEU* 1.3 90.5 + - - +
3345 GLU* 1.3 65.6 + - + +
3355 LEU 3.4 2.5 - - - -
3365 GLY 5.1 0.4 - - - -
3375 TYR* 4.1 12.1 + - - -
3575 PHE* 4.6 11.2 - - + -
3585 LYS* 4.8 6.9 + - - +
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Residues in contact with GLU 334 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3084 LEU* 5.3 1.3 - - - -
1185 LYS* 5.3 10.7 - - - +
1205 LYS* 3.1 26.3 + - - -
3305 PRO* 6.0 2.2 - - + -
3315 PRO* 3.1 36.1 + - + +
3335 GLU* 1.3 82.5 - - + +
3355 LEU* 1.3 58.8 + - - +
3365 GLY 3.1 4.0 + - - +
3375 TYR* 3.1 47.6 + - + +
3385 HIS* 5.8 0.2 + - - -
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Residues in contact with LEU 335 (chain 5).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2984 ALA* 5.0 2.7 - - + -
3004 VAL* 4.2 15.8 - - + +
3034 PRO* 4.3 4.9 - - + -
3084 LEU* 3.4 47.8 - - + +
3114 ASN* 4.4 11.2 - - + +
3124 SER* 3.5 13.9 - - - +
1205 LYS* 4.1 8.1 - - - +
3315 PRO 4.3 0.6 + - - -
3325 LEU* 3.4 15.6 + - + +
3335 GLU 3.4 2.2 - - - -
3345 GLU* 1.3 78.0 - - - +
3365 GLY* 1.3 60.3 + - - +
3375 TYR 3.3 0.2 - - - -
3485 VAL* 5.9 0.2 - - + -
3575 PHE* 3.3 46.2 - - + -
1026 TYR* 3.0 22.8 + - - +
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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