Contacts of the strand formed by residues 342 - 346 (chain C) in PDB entry 1K4R
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 VAL 342 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328C MET* 5.4 0.4 - - - -
340C ILE* 3.2 31.9 + - + +
341C PRO* 1.3 71.9 - - - +
343C ARG* 1.3 68.3 + - - +
353C ASN* 4.5 4.9 + - - -
355C ALA* 5.6 0.8 - - - +
357C LEU* 4.6 17.4 - - + +
362C PRO* 4.2 15.7 - - + -
372C ILE* 3.9 22.2 - - + -
374C MET* 3.6 29.4 - - + -
383C ILE* 5.0 1.3 - - + -
384C TYR 3.3 9.6 - - - +
385C VAL* 4.1 9.2 - - + +
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Residues in contact with ARG 343 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341C PRO 5.3 2.4 + - - +
342C VAL* 1.3 79.3 - - - +
344C ALA* 1.3 65.8 + - - +
345C VAL* 3.7 24.8 - - + +
350C PRO 4.0 9.5 + - - -
353C ASN* 3.7 28.7 - - + +
355C ALA* 4.2 7.2 - - - -
374C MET* 5.4 0.7 - - - -
383C ILE* 3.8 4.2 - - - +
384C TYR* 2.8 72.3 + - + +
386C GLY 4.8 5.5 + - - +
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Residues in contact with ALA 344 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ARG* 1.3 79.6 - - - +
345C VAL* 1.3 61.2 - - - +
353C ASN* 3.2 10.7 + - - +
354C VAL* 2.7 30.5 + - + -
355C ALA* 3.8 8.5 - - + +
374C MET* 4.7 1.8 - - - -
376C LEU* 3.4 33.0 - - + -
381C ASN* 5.2 0.9 - - + -
382C ILE 3.2 14.1 - - - +
383C ILE* 4.2 10.5 - - + -
384C TYR* 5.0 0.4 - - - -
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Residues in contact with VAL 345 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343C ARG* 3.7 19.5 - - + +
344C ALA* 1.3 77.8 - - - +
346C ALA* 1.3 67.0 + - - +
349C SER 3.5 11.0 - - - +
350C PRO* 3.5 33.2 - - + +
352C VAL 3.7 14.6 - - - +
353C ASN* 4.8 1.8 - - - -
354C VAL* 4.0 5.8 - - - -
381C ASN* 3.2 3.8 - - - +
382C ILE* 2.9 41.6 + - + +
384C TYR* 4.0 20.9 - - + +
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Residues in contact with ALA 346 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345C VAL* 1.3 79.6 - - - +
347C HIS* 1.3 69.4 + - - +
348C GLY 3.1 0.7 + - - -
349C SER* 3.0 33.7 + - - +
352C VAL 4.5 0.2 + - - -
354C VAL* 4.0 17.8 - - + +
377C PRO* 5.6 3.1 - - + -
380C ASP 3.7 7.4 - - - +
381C ASN* 3.9 9.9 - - - +
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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