Contacts of the helix formed by residues 334 - 338 (chain A) in PDB entry 1KAS
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 334 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A LEU* 3.9 18.6 - - + +
299A TYR* 4.3 3.6 - - - +
301A ASN* 3.5 19.2 + - - +
302A ALA 5.4 0.2 + - - -
332A SER* 4.0 4.0 + - - +
333A SER* 1.3 68.9 - - - +
335A LYS* 1.3 55.2 + - - +
336A SER 3.2 5.2 - - - -
337A MET* 3.3 17.0 + - + +
338A THR* 3.1 29.3 + - - +
349A GLU* 4.0 9.4 - - - +
352A TYR* 3.3 27.9 - - + -
363A PRO* 3.8 33.9 - - + -
364A PRO 4.8 0.2 - - - +
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Residues in contact with LYS 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A SER* 2.6 22.3 + - - +
221A PRO* 5.2 0.2 - - - -
302A ALA 4.0 1.2 + - - +
303A HIS* 2.8 37.9 + - - +
304A GLY 3.6 7.6 - - - +
305A THR* 4.0 11.9 - - + -
333A SER* 3.1 11.3 - - - +
334A THR* 1.3 75.3 - - - +
336A SER* 1.3 52.6 + - - +
337A MET 3.2 1.1 - - - -
338A THR* 3.9 1.1 - - + -
339A GLY* 3.0 38.1 + - - +
340A HIS* 3.2 48.2 - - + +
345A ALA* 4.0 5.1 - - - +
349A GLU* 2.5 43.6 + - - +
397A SER* 5.5 0.4 + - - -
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Residues in contact with SER 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A SER* 4.7 2.8 + - - -
34A ILE* 5.2 1.6 - - - +
216A GLN 4.7 2.1 - - - +
219A SER* 3.2 25.6 + - - +
221A PRO* 3.7 17.2 - - - +
333A SER* 2.7 24.0 + - - -
335A LYS* 1.3 77.6 - - - +
337A MET* 1.3 58.6 + - - +
364A PRO 3.8 2.9 + - - -
365A THR* 3.5 1.1 - - - -
366A ILE* 3.1 57.0 + - - +
367A ASN* 3.9 1.9 + - - -
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Residues in contact with MET 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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16A VAL* 4.4 1.1 - - - +
27A LEU* 3.3 50.9 - - + +
30A GLY* 3.5 17.0 - - - -
31A GLN 3.1 22.7 - - - +
32A SER* 3.7 4.8 - - - +
33A GLY* 2.8 28.4 + - - -
34A ILE* 3.9 7.5 - - - +
334A THR* 3.3 25.3 + - + +
336A SER* 1.3 80.1 - - - +
338A THR* 1.3 60.9 + - - +
339A GLY 3.6 0.2 - - - -
364A PRO* 3.1 31.4 - - + +
366A ILE* 3.6 23.8 - - + -
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Residues in contact with THR 338 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A SER* 4.5 2.8 + - - -
15A PRO* 3.4 44.4 - - - +
16A VAL* 4.6 7.6 - - - +
27A LEU* 4.8 7.0 - - - -
34A ILE* 3.8 9.6 - - - +
51A GLY* 4.2 2.9 - - - -
232A GLY* 4.2 0.7 - - - -
334A THR* 3.1 21.3 + - - +
335A LYS* 3.9 5.2 - - + +
337A MET* 1.3 80.3 - - - +
339A GLY* 1.3 73.8 + - - +
341A LEU* 3.8 15.6 - - + +
348A VAL* 5.5 1.8 - - + -
349A GLU* 5.3 3.4 - - - +
352A TYR* 3.9 21.2 + - + +
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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