Contacts of the strand formed by residues 321 - 327 (chain B) in PDB entry 4KIK
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 THR 321 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314B ILE 3.7 0.9 - - - +
315B LEU* 3.7 0.8 - - - -
316B ASN* 3.0 25.7 + - - +
319B THR* 3.5 23.4 + - - +
320B GLY* 1.4 82.7 - - - +
322B ILE* 1.3 63.8 + - - +
323B HIS* 3.3 27.3 + - - -
401B ILE 5.9 0.4 - - - +
402B SER* 6.1 0.9 - - - +
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Residues in contact with ILE 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASN* 6.5 0.2 - - + -
267B SER* 5.3 6.8 - - - -
313B HIS* 4.1 24.5 - - + +
314B ILE 3.3 8.7 - - - +
315B LEU* 4.3 20.4 - - + -
320B GLY 4.9 4.9 - - - +
321B THR* 1.3 75.7 - - - +
323B HIS* 1.3 64.2 + - - +
324B THR* 4.0 12.8 + - - +
382B LEU* 4.2 17.5 - - + -
386B LEU* 4.4 2.2 - - + -
404B ARG* 4.0 23.3 - - - +
443B ASP* 5.2 2.7 - - - +
446B ARG* 3.8 30.5 - - - +
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Residues in contact with HIS 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B VAL 3.5 2.1 - - - +
313B HIS* 3.5 1.6 - - - -
314B ILE* 2.8 48.4 + - + +
316B ASN* 4.2 7.9 + - + +
319B THR* 4.9 1.1 - - - -
321B THR* 3.3 30.8 + - - -
322B ILE* 1.3 72.2 - - - +
324B THR* 1.3 60.8 + - - +
325B TYR* 3.5 28.8 - - + +
343B ASP* 3.6 36.1 + - + +
344B THR* 3.6 28.4 - - + +
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Residues in contact with THR 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
266B ASN* 3.6 27.6 - - - +
267B SER* 4.5 14.4 - - - -
268B VAL* 3.6 30.6 - - + +
311B LEU* 4.1 11.7 - - + -
312B VAL 3.3 4.7 - - - +
313B HIS* 2.9 34.0 + - + +
322B ILE* 4.0 9.5 + - - +
323B HIS* 1.3 73.0 - - - +
325B TYR* 1.3 69.8 + - - +
326B PRO* 4.0 1.0 - - - +
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Residues in contact with TYR 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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311B LEU* 4.3 2.7 - - - -
312B VAL* 2.9 35.3 + - + +
314B ILE* 4.1 10.5 - - + -
323B HIS* 3.5 35.2 - - + +
324B THR* 1.3 78.7 - - - +
326B PRO* 1.4 67.4 - - - +
327B VAL* 3.2 3.5 + - - +
336B LEU* 3.8 29.8 - - + -
339B ARG* 3.8 41.1 - - + +
340B ILE* 3.3 35.4 - - + +
343B ASP* 2.7 37.2 + - - +
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Residues in contact with PRO 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B VAL* 3.9 29.6 - - + -
309B LEU* 3.8 25.6 - - + -
310B LYS 3.8 0.9 - - - +
311B LEU* 3.6 11.4 - - + -
324B THR 4.0 5.6 - - - +
325B TYR* 1.4 79.2 - - - +
327B VAL* 1.3 55.3 + - - +
328B THR* 5.8 0.6 - - - +
331B GLU* 3.8 1.7 - - - +
339B ARG* 2.8 42.9 + - - +
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Residues in contact with VAL 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B LEU* 6.0 0.9 - - - +
310B LYS* 2.9 34.1 + - + +
312B VAL* 4.4 6.3 - - + -
325B TYR 3.2 5.4 + - - +
326B PRO* 1.3 74.9 - - - +
328B THR* 1.3 63.5 + - - +
331B GLU* 3.4 24.2 - - + +
336B LEU* 4.3 14.4 - - + -
339B ARG* 4.5 0.2 - - - +
367B ALA* 3.4 27.8 - - + -
368B THR* 3.6 35.4 - - + +
371B ILE* 4.3 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