Contacts of the strand formed by residues 312 - 320 (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 PHE 312 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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307C CYS* 3.4 38.8 - - + -
308C ASP 3.7 13.0 - - - -
309C LYS* 4.6 5.8 + - - +
310C THR 3.6 5.0 - - - +
311C LYS* 1.3 77.2 - - - +
313C THR* 1.3 68.6 + - - +
330C VAL* 3.7 18.6 - - + -
331C THR 3.3 7.9 - - - -
332C PHE* 3.5 22.2 - + + -
340C ILE* 3.9 22.4 - - + -
341C PRO* 3.8 15.5 - - + -
364C ILE* 4.1 7.2 - - + -
385C VAL* 3.6 30.1 - - + +
388C LEU* 3.8 30.7 - - + +
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Residues in contact with THR 313 (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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311C LYS 5.1 2.0 + - - +
312C PHE* 1.3 80.4 - - - +
314C TRP* 1.3 63.7 + - - +
330C VAL* 3.3 7.4 - - - +
331C THR* 2.9 45.7 + - - +
388C LEU* 3.6 12.3 - - + -
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Residues in contact with TRP 314 (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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313C THR* 1.3 76.0 - - - +
315C LYS* 1.3 60.9 + - - +
316C ARG 4.0 9.2 - - - -
317C ALA* 4.4 16.6 - - + +
318C PRO* 4.0 22.0 - - + -
328C MET* 3.8 22.9 - - + -
329C GLU 3.9 1.1 - - - -
330C VAL* 3.6 27.4 - - + -
331C THR* 5.1 0.7 - - - -
383C ILE* 4.0 14.8 - - + -
385C VAL* 3.8 20.0 - - + -
388C LEU* 3.4 29.6 - - + +
389C SER* 3.2 23.2 + - - -
390C HIS* 3.5 34.2 - + + -
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Residues in contact with LYS 315 (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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313C THR 3.7 2.4 + - - -
314C TRP* 1.3 74.0 - - - +
316C ARG* 1.3 66.3 + - + +
317C ALA 4.2 0.7 - - - -
329C GLU* 2.7 45.9 + - + +
330C VAL 4.5 2.2 - - - -
331C THR* 3.3 34.0 + - - +
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Residues in contact with ARG 316 (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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101B TRP* 3.6 70.5 + - + +
105B CYS 5.4 0.2 + - - -
150C TYR* 3.5 25.4 + - - +
314C TRP* 4.0 2.8 - - - -
315C LYS* 1.3 87.2 - - + +
317C ALA* 1.3 67.3 + - - +
328C MET* 3.5 3.1 - - - +
329C GLU* 3.0 54.2 + - - +
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Residues in contact with ALA 317 (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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101B TRP* 4.4 0.9 - - - -
314C TRP* 4.4 13.0 - - + +
315C LYS 4.2 0.6 - - - -
316C ARG* 1.3 77.1 - - - +
318C PRO* 1.3 80.7 - - + +
319C THR* 3.3 10.2 + - - +
327C VAL 3.9 2.3 - - - +
390C HIS* 3.9 18.4 - - + +
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Residues in contact with PRO 318 (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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314C TRP* 4.0 25.1 - - + -
316C ARG 3.8 0.4 - - - -
317C ALA* 1.3 91.0 - - + +
319C THR* 1.3 58.9 + - - +
326C VAL* 3.8 17.9 - - + -
327C VAL 3.3 9.4 - - - +
328C MET* 3.9 5.8 - - + -
383C ILE* 3.9 22.7 - - + -
390C HIS* 3.6 33.1 - - + +
392C TRP* 3.5 23.4 - - + -
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Residues in contact with THR 319 (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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101B TRP* 3.2 42.2 - - + +
106B GLY 4.0 4.8 + - - -
107B LEU* 3.6 27.8 - - - +
108B PHE* 4.0 7.2 - - + -
317C ALA 3.9 3.8 - - - -
318C PRO* 1.3 76.5 - - - +
320C ASP* 1.3 66.2 + - - +
321C SER 3.4 0.2 + - - -
326C VAL* 3.5 4.3 - - - +
327C VAL* 2.9 40.7 + - + +
392C TRP* 3.9 8.5 - - - -
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Residues in contact with ASP 320 (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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107B LEU* 6.4 1.1 - - + -
108B PHE* 3.2 29.7 + - - +
319C THR* 1.3 76.0 + - - +
321C SER* 1.3 61.7 + - - +
322C GLY* 3.3 17.0 + - - -
324C ASP* 4.8 7.9 + - - +
325C THR 4.0 8.2 - - - +
392C TRP* 3.6 25.7 - - + -
394C GLN* 4.9 9.5 + - - -
395C 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