Contacts of the strand formed by residues 333 - 342 (chain A) in PDB entry 3KYS
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 ARG 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A ARG* 5.0 9.6 - - - +
296A GLN* 5.1 0.2 - - - +
298A GLU* 3.1 45.4 + - - -
299A SER 3.8 11.9 - - - +
300A SER* 5.3 3.8 - - - +
328A ARG 3.5 0.3 - - - +
329A PHE* 3.3 10.5 - - - -
330A GLU* 2.6 49.7 + - - +
331A ASN* 3.1 42.3 + - - +
332A GLY* 1.3 73.6 - - - +
334A PHE* 1.3 59.0 + - - +
335A VAL* 3.3 18.2 + - + +
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Residues in contact with PHE 334 (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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298A GLU* 3.7 1.0 - - - +
299A SER* 2.7 41.3 + - - +
300A SER* 3.7 21.3 - - - -
301A GLU* 3.6 23.6 - - - +
302A ASN* 3.7 35.9 - - + -
327A ALA* 3.7 24.5 - - + -
328A ARG 3.4 3.1 - - - -
329A PHE* 3.6 35.7 - + + -
332A GLY 5.8 0.2 - - - -
333A ARG* 1.3 73.2 - - - +
335A VAL* 1.3 58.1 + - - +
336A TYR* 3.8 4.5 - - - +
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Residues in contact with VAL 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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296A GLN* 3.6 30.7 - - + +
297A TYR 3.5 9.4 - - - +
298A GLU* 3.7 9.9 - - + +
326A TYR 3.9 0.9 - - - +
328A ARG* 2.6 43.3 + - - +
330A GLU* 4.2 24.2 - - + +
333A ARG* 3.3 35.4 - - + +
334A PHE* 1.3 76.6 - - - +
336A TYR* 1.3 67.6 + - - +
337A ARG* 4.0 7.6 + - + -
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Residues in contact with TYR 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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201A LEU* 4.0 13.5 - - + -
297A TYR* 2.6 62.4 + - + +
299A SER* 3.4 24.7 - - - -
301A GLU 2.6 25.2 + - - -
302A ASN* 3.7 1.2 - - - -
303A MET* 3.1 39.6 + - + +
305A VAL* 3.6 31.9 - - + -
325A GLU* 3.8 17.5 - - + -
326A TYR* 3.6 19.3 - - - -
327A ALA* 3.5 16.6 - - + +
334A PHE 3.8 9.4 - - - -
335A VAL* 1.3 73.3 - - - +
337A ARG* 1.3 55.4 + - - +
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Residues in contact with ARG 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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205A GLU* 4.6 2.4 + - - -
294A THR* 3.7 22.2 + - - +
295A SER 3.5 9.4 - - - +
296A GLN* 4.0 31.1 + - + -
325A GLU* 3.2 22.2 + - - +
335A VAL* 4.0 7.9 + - + +
336A TYR* 1.3 75.5 - - - +
338A ILE* 1.3 69.2 + - - +
339A ASN* 2.9 44.3 + - - +
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Residues in contact with ILE 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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293A VAL 4.9 0.4 - - - +
294A THR* 3.5 12.2 - - - +
295A SER* 2.7 52.0 + - - +
297A TYR* 4.2 8.7 - - + -
307A CYS* 4.1 16.8 - - + -
323A GLU* 3.5 43.3 - - + +
325A GLU* 3.6 35.2 - - + +
337A ARG* 1.3 73.3 - - - +
339A ASN* 1.3 60.2 + - - +
341A SER* 3.6 18.6 - - - -
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Residues in contact with ASN 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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294A THR* 4.4 0.4 + - - -
337A ARG* 2.9 44.3 + - - +
338A ILE* 1.3 73.5 - - - +
340A ARG* 1.3 93.0 + - - +
341A SER* 3.4 1.2 + - - -
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Residues in contact with ARG 340 (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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209A PHE* 4.1 13.4 - - + -
211A GLU* 2.5 46.5 + - - -
221A LYS* 5.5 1.6 - - - +
290A PHE* 3.3 40.3 - - + +
293A VAL 4.3 0.2 - - - -
294A THR* 3.1 22.6 + - - +
338A ILE 3.8 1.0 + - - -
339A ASN* 1.3 95.6 - - - +
341A SER* 1.3 64.1 + - - +
342A PRO* 3.5 4.3 - - - +
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Residues in contact with SER 341 (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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292A GLY* 3.1 1.4 - - - -
293A VAL* 2.5 48.8 + - - +
321A LYS* 2.7 25.3 + - - -
323A GLU* 3.1 25.7 + - - -
338A ILE* 3.6 15.3 - - - -
339A ASN 3.4 1.9 - - - -
340A ARG* 1.3 76.0 - - - +
342A PRO* 1.4 63.8 - - - +
343A MET 3.6 0.2 + - - -
53B GLN* 3.2 3.1 + - - -
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Residues in contact with PRO 342 (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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290A PHE* 3.9 19.5 - - + -
291A TYR 3.6 8.5 - - - +
321A LYS* 2.8 24.5 + - - +
340A ARG 3.5 7.5 - - - +
341A SER* 1.4 82.5 - - - +
343A MET* 1.3 63.2 + - - +
53B GLN* 3.2 35.7 + - - +
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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