Contacts of the helix formed by residues 334 - 339 (chain A) in PDB entry 4IKV
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 SER 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A GLY 3.9 3.4 + - - -
181A MET* 3.4 26.4 - - - +
182A LYS* 3.7 17.7 - - - +
332A HIS* 3.6 2.3 + - - -
333A LEU* 1.3 74.6 - - - +
335A PRO* 1.3 70.6 - - - +
336A ALA* 3.4 12.6 + - - +
337A TRP* 2.9 53.6 + - - +
338A PHE* 4.2 4.3 - - - -
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Residues in contact with PRO 335 (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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48A TYR* 3.4 31.5 + - + +
52A TYR* 4.5 5.4 - - - +
181A MET* 4.6 8.3 - - + -
320A ALA* 3.9 7.8 - - + +
321A ASP* 3.8 39.5 - - - +
326A LEU* 4.3 12.1 - - + -
332A HIS* 5.3 2.7 - - - +
333A LEU 3.8 6.0 - - - +
334A SER* 1.3 88.7 - - - +
336A ALA* 1.3 62.0 + - - +
337A TRP 3.2 0.3 + - - -
338A PHE* 3.3 31.2 + - + +
339A GLN* 4.7 2.6 + - - -
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Residues in contact with ALA 336 (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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44A ALA* 3.4 28.0 - - + +
48A TYR* 3.8 5.9 - - + -
173A PRO* 3.5 6.8 - - - +
177A GLY* 3.9 24.7 - - - -
181A MET* 4.0 9.9 - - + -
334A SER* 3.1 13.4 + - - +
335A PRO* 1.3 80.6 - - - +
337A TRP* 1.3 63.6 + - - +
338A PHE 3.1 1.4 + - - -
339A GLN* 3.1 23.2 + - - +
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Residues in contact with TRP 337 (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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173A PRO* 3.4 23.8 + - - -
174A LEU* 4.0 22.2 - - + +
178A THR* 3.1 32.8 + - + +
182A LYS* 3.7 29.4 - - - -
331A ILE* 5.6 3.4 - - + -
332A HIS 4.0 2.2 - - - -
333A LEU* 3.6 28.7 - - + -
334A SER* 2.9 44.1 + - - +
336A ALA* 1.3 78.3 - - + +
338A PHE* 1.3 58.7 + - + +
339A GLN 3.0 0.7 - - - -
340A SER* 2.9 27.2 + - - -
341A LEU* 4.2 2.8 + - - +
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Residues in contact with PHE 338 (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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320A ALA* 3.8 13.2 - - + -
324A THR* 4.3 8.1 - - + -
326A LEU* 4.2 20.9 - - + -
333A LEU* 4.3 13.9 - - + -
334A SER 4.2 4.7 - - - -
335A PRO* 3.3 22.1 + - + +
336A ALA 3.1 1.8 + - - -
337A TRP* 1.3 78.4 - - + +
339A GLN* 1.3 59.2 + - - +
340A SER 3.1 1.3 - - - -
341A LEU* 3.1 46.5 + - + +
342A ASN 4.5 0.3 + - - -
399A PRO* 3.8 29.2 - - + -
402A LEU* 3.8 33.4 - - + -
403A VAL* 4.2 10.5 - - + -
406A TYR* 3.9 24.4 - - + +
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Residues in contact with GLN 339 (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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40A TYR 5.7 0.4 - - - +
43A ARG 5.5 1.1 - - - +
44A ALA* 4.2 21.5 - - + +
48A TYR* 6.1 0.4 - - + +
169A ALA* 4.0 4.3 - - - +
173A PRO* 3.7 17.0 - - + -
312A GLY 3.0 23.4 + - - +
313A SER* 3.2 32.0 + - - +
317A ALA* 3.9 16.8 - - + +
335A PRO 5.3 1.2 + - - -
336A ALA* 3.4 17.0 - - - +
337A TRP 3.0 0.8 - - - -
338A PHE* 1.3 80.6 - - - +
340A SER* 1.3 57.7 + - - +
341A LEU 3.3 0.2 - - - -
342A ASN* 4.4 2.8 + - - +
343A PRO* 3.4 16.6 - - - +
406A TYR* 3.4 14.0 + - - -
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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