Contacts of the strand formed by residues 312 - 320 (chain A) 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 PHE 312 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307A CYS* 3.4 38.6 - - + -
308A ASP 3.7 12.8 - - - -
309A LYS 4.6 5.8 + - - +
310A THR 3.6 4.8 - - - +
311A LYS* 1.3 77.7 - - - +
313A THR* 1.3 67.7 - - - +
330A VAL* 3.7 19.1 - - + -
331A THR 3.3 8.1 - - - -
332A PHE* 3.5 22.2 - + + -
340A ILE* 3.9 22.4 - - + -
341A PRO* 3.8 15.7 - - + -
364A ILE* 4.1 6.3 - - + -
385A VAL* 3.6 30.5 - - + +
388A LEU* 3.8 30.9 - - + +
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Residues in contact with THR 313 (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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311A LYS 5.1 3.0 + - - +
312A PHE* 1.3 79.9 - - - +
314A TRP* 1.3 63.3 + - - +
330A VAL* 3.3 7.1 - - - +
331A THR* 2.9 46.8 + - - +
388A LEU* 3.6 12.3 - - + -
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Residues in contact with TRP 314 (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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313A THR* 1.3 76.0 - - - +
315A LYS* 1.3 59.8 + - - +
316A ARG 4.0 9.9 - - - -
317A ALA* 4.4 16.6 - - + +
318A PRO* 4.0 21.1 - - + -
328A MET* 3.8 23.1 - - + -
329A GLU 3.9 0.9 - - - -
330A VAL* 3.6 26.7 - - + -
331A THR* 5.1 0.4 - - - -
383A ILE* 4.0 14.6 - - + -
385A VAL* 3.8 19.3 - - + -
388A LEU* 3.4 30.0 - - + +
389A SER* 3.2 23.4 + - - -
390A HIS* 3.5 33.5 - + + -
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Residues in contact with LYS 315 (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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313A THR 3.7 3.0 + - - -
314A TRP* 1.3 74.3 - - - +
316A ARG* 1.3 66.2 + - + +
317A ALA 4.2 0.4 - - - -
329A GLU* 2.7 45.6 + - + +
330A VAL 5.0 1.8 - - - -
331A THR* 3.3 33.2 + - - +
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Residues in contact with ARG 316 (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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150A TYR* 3.5 39.0 + - - +
314A TRP* 4.0 2.4 - - - -
315A LYS* 1.3 87.7 - - + +
317A ALA* 1.3 69.1 + - - +
319A THR* 6.4 1.1 - - + -
328A MET* 3.5 6.6 - - - +
329A GLU* 3.0 60.1 + - - +
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Residues in contact with ALA 317 (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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314A TRP* 4.4 13.0 - - + +
315A LYS 4.2 1.0 - - - -
316A ARG* 1.3 77.2 - - - +
318A PRO* 1.3 81.2 - - + +
319A THR* 3.3 10.6 + - - +
327A VAL 3.9 2.3 - - - +
328A MET* 4.4 0.2 - - - -
390A HIS* 3.9 17.9 - - + +
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Residues in contact with PRO 318 (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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314A TRP* 4.0 25.1 - - + -
316A ARG 3.8 0.2 - - - -
317A ALA* 1.3 91.2 - - + +
319A THR* 1.3 59.9 + - - +
326A VAL* 3.8 17.5 - - + -
327A VAL 3.3 9.6 - - - +
328A MET* 3.9 5.1 - - + -
383A ILE* 3.9 22.0 - - + -
390A HIS* 3.6 33.1 - - + +
392A TRP* 3.5 22.5 - - + -
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Residues in contact with THR 319 (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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316A ARG* 6.4 1.6 - - + -
317A ALA 3.9 6.5 - - - +
318A PRO* 1.3 76.1 - - - +
320A ASP* 1.3 71.4 + - - +
321A SER 3.4 0.3 + - - -
326A VAL* 3.5 4.5 - - - +
327A VAL* 2.9 53.5 + - + +
328A MET* 5.9 0.2 - - - -
392A TRP* 3.9 8.1 - - - -
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Residues in contact with ASP 320 (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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319A THR* 1.3 83.1 + - - +
321A SER* 1.3 63.0 + - - +
322A GLY* 3.3 17.3 + - - -
324A ASP* 4.8 7.0 + - - +
325A THR 4.0 7.5 - - - +
392A TRP* 3.6 25.7 - - + -
394A GLN* 4.9 9.5 + - - -
395A LYS* 5.0 9.2 + - - +
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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