Contacts of the helix formed by residues 303 - 308 (chain A) in PDB entry 2IHU
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 ARG 303 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A TYR* 3.8 1.3 - - - -
298A TYR* 3.9 30.5 - - + -
301A ASP* 3.2 38.2 + - - +
302A LEU* 1.3 75.6 - - - +
304A PRO* 1.4 75.8 - - + +
305A SER* 4.1 19.0 + - - +
306A MET* 3.0 51.1 + - + +
307A TRP* 3.8 7.5 - - - -
328A VAL* 5.7 0.7 - - + -
570A ALA 4.0 10.7 + - - -
571A LEU* 3.6 28.7 + - - +
572A SER 4.7 4.8 - - - -
113B ASP* 5.5 2.2 - - - -
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Residues in contact with PRO 304 (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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296A TYR* 3.4 12.3 - - - +
298A TYR* 4.4 1.6 - - + -
303A ARG* 1.4 87.6 - - + +
305A SER* 1.3 62.0 + - - +
306A MET 3.0 1.4 + - - -
307A TRP* 3.1 43.7 + - + -
308A GLN* 3.1 34.0 + - - +
328A VAL* 3.9 36.6 - - + +
329A TYR* 3.9 18.8 - - + -
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Residues in contact with SER 305 (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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303A ARG* 3.2 23.5 + - - +
304A PRO* 1.3 78.9 - - - +
306A MET* 1.3 65.3 + - - +
308A GLN* 3.5 25.8 + - - +
309A LYS* 3.5 17.5 + - - -
570A ALA 5.0 3.8 + - - -
572A SER 5.8 3.6 - - - -
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Residues in contact with MET 306 (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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251A TYR* 6.0 0.4 - - - +
268A VAL* 4.1 26.9 - - + +
269A THR* 5.3 0.2 - - - -
270A GLY* 3.8 31.2 - - - +
281A LEU* 3.8 11.4 - - + +
285A PHE* 3.4 16.6 - - - -
301A ASP* 3.5 17.3 - - - +
302A LEU* 4.0 7.9 - - + -
303A ARG* 3.0 65.7 + - + +
304A PRO 3.0 0.2 + - - -
305A SER* 1.3 85.5 - - - +
307A TRP* 1.3 57.3 + - - +
308A GLN 3.3 0.2 - - - -
309A LYS* 3.4 20.9 - - - +
570A ALA 5.1 6.5 - - - +
571A LEU* 5.9 0.7 - - + -
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Residues in contact with TRP 307 (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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222A VAL* 5.3 1.8 - - + -
285A PHE* 3.6 36.5 - - + +
291A VAL* 3.9 28.3 - - + -
293A THR* 3.8 25.4 - - + -
296A TYR* 4.0 16.4 - + - -
302A LEU* 3.8 17.0 - - + -
303A ARG 3.8 11.6 + - - -
304A PRO* 3.1 45.1 + - + +
306A MET* 1.3 76.5 - - - +
308A GLN* 1.3 73.5 + - + +
309A LYS 2.9 11.9 + - - -
313A LYS* 3.1 27.0 - - + +
315A THR* 3.6 21.5 - - + +
329A TYR* 3.7 29.6 - + - -
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Residues in contact with GLN 308 (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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304A PRO* 3.1 28.2 + - - +
305A SER* 3.5 26.1 + - - +
306A MET 3.3 2.6 - - - -
307A TRP* 1.3 88.5 + - + +
309A LYS* 1.3 67.3 + - - +
311A ILE 5.6 0.2 - - - -
313A LYS* 4.7 7.0 - - + -
328A VAL 5.6 0.5 - - - +
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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