Contacts of the helix formed by residues 305 - 310 (chain H) in PDB entry 3EXF
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 ALA 305 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 4.1 0.4 - - - +
111E GLY* 4.0 17.5 - - - +
119E GLY* 2.8 21.7 + - - +
329E GLU* 4.1 5.6 - - - +
330E PRO* 3.9 27.1 - - + -
303H PRO* 4.9 0.6 - - - +
304H TYR* 1.3 74.8 - - - +
306H LYS* 1.3 58.5 + - - +
307H ILE* 3.4 1.1 - - + -
308H LEU* 3.0 28.9 + - + +
309H GLU 3.0 10.9 + - - -
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Residues in contact with LYS 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 3.5 46.2 - - - +
329E GLU* 3.0 14.1 + - - +
304H TYR 3.0 5.7 + - - -
305H ALA* 1.3 65.9 - - - +
307H ILE* 1.3 66.2 + - - +
309H GLU* 4.6 1.6 - - - +
310H ASP* 2.9 61.2 + - - +
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Residues in contact with ILE 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329E GLU* 2.9 36.7 + - + +
330E PRO 3.7 25.6 - - - +
331E PRO* 5.4 0.9 - - + +
332E LEU* 4.8 18.4 - - + +
305H ALA* 4.4 4.3 - - + +
306H LYS* 1.3 73.0 - - - +
308H LEU* 1.3 77.2 + - + +
310H ASP* 3.9 4.7 - - - +
311H ASN* 2.5 43.1 + - - +
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Residues in contact with LEU 308 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLY 4.7 1.6 - - - +
120E LYS* 3.7 30.7 - - + -
330E PRO* 3.9 21.1 - - + -
331E PRO 3.8 18.6 - - - +
332E LEU* 4.1 8.5 - - + -
334E GLU 5.5 0.2 - - - +
335E LEU* 3.6 32.8 - - + +
303H PRO* 3.6 17.3 - - + -
305H ALA* 3.0 18.3 + - + +
307H ILE* 1.3 86.0 - - + +
309H GLU* 1.3 64.3 + - - +
310H ASP 3.1 1.3 - - - -
311H ASN* 3.1 13.3 + - - +
312H SER* 2.8 19.8 + - - -
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Residues in contact with GLU 309 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ARG* 3.0 22.4 + - - +
121H SER 4.4 5.2 - - - +
122H ALA* 3.6 6.9 - - - +
123H GLY* 2.7 43.0 + - - -
124H VAL* 3.9 2.3 + - - +
302H MET* 4.1 19.7 - - + +
303H PRO* 3.5 25.8 - - - +
304H TYR 4.2 0.2 - - - +
305H ALA 3.0 13.7 + - - +
306H LYS* 4.1 3.1 - - - +
308H LEU* 1.3 75.8 - - - +
310H ASP* 1.3 64.4 + - - +
312H SER* 3.3 13.7 - - - -
313H ILE* 3.2 30.1 - - + +
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Residues in contact with ASP 310 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306H LYS* 2.9 58.0 + - - +
307H ILE* 3.9 7.1 - - - +
309H GLU* 1.3 81.2 - - - +
311H ASN* 1.3 56.1 + - - +
312H SER 3.3 2.7 - - - -
313H ILE* 3.5 10.2 - - - +
315H GLN* 2.6 46.3 + - - +
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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