Contacts of the helix formed by residues 323 - 335 (chain A) in PDB entry 6KSF
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 SER 323 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A SER* 1.3 82.2 - - - +
324A VAL* 1.3 63.5 + - - +
325A GLU* 3.8 7.4 - - - -
326A ASP* 3.6 30.5 + - - +
327A TRP* 3.1 23.0 + - - +
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Residues in contact with VAL 324 (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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322A SER 3.7 2.0 + - - +
323A SER* 1.3 73.6 - - - +
325A GLU* 1.3 62.1 + - + +
327A TRP* 4.6 2.5 - - - +
328A GLN* 2.3 49.4 + - - +
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Residues in contact with GLU 325 (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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148A LYS* 3.3 35.5 + - + +
151A LEU* 6.6 0.2 - - + -
152A ARG* 3.8 29.1 + - + +
323A SER* 3.2 7.7 - - - -
324A VAL* 1.3 83.9 - - + +
326A ASP* 1.3 65.8 + - - +
328A GLN* 3.2 6.5 + - - +
329A VAL* 3.0 29.8 + - + +
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Residues in contact with ASP 326 (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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116A LYS* 4.4 16.8 + - + +
120A LYS* 2.9 24.3 + - - +
144A TRP* 2.8 37.6 + - + +
148A LYS* 4.2 9.4 + - - +
322A SER* 4.6 1.1 - - - -
323A SER* 3.5 29.6 + - - +
324A VAL 3.4 0.4 - - - -
325A GLU* 1.3 78.3 - - - +
327A TRP* 1.3 57.1 + - - +
329A VAL* 3.3 4.8 + - - +
330A CYS* 2.9 33.2 + - - -
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Residues in contact with TRP 327 (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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112A ARG* 3.5 50.5 - - + +
115A VAL* 4.6 7.9 - - + -
116A LYS* 6.0 0.4 - - + -
301A LEU* 4.2 12.3 - - + +
305A LEU* 3.6 33.8 + - + -
306A GLU* 5.4 4.1 - - + +
322A SER* 5.0 9.6 + - - +
323A SER 3.1 18.6 + - - +
324A VAL* 4.1 3.4 - - - +
326A ASP* 1.3 73.8 - - - +
328A GLN* 1.3 78.5 + - - +
330A CYS* 3.6 22.4 - - + -
331A ALA* 2.8 48.2 + - + +
334A LEU* 4.6 4.7 - - + -
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Residues in contact with GLN 328 (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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151A LEU* 4.1 16.6 - - + -
324A VAL* 2.3 55.5 + - - +
325A GLU* 3.2 7.2 + - - +
327A TRP* 1.3 91.7 + - - +
329A VAL* 1.3 65.5 + - - +
331A ALA* 3.9 6.0 - - - +
332A THR* 3.0 32.5 + - + +
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Residues in contact with VAL 329 (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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144A TRP* 3.5 29.6 - - + -
147A SER* 3.8 21.3 - - - -
148A LYS* 4.0 28.7 - - + -
151A LEU* 3.9 22.0 - - + -
165A LEU* 4.0 8.1 - - + -
325A GLU* 3.0 16.4 + - + +
326A ASP 3.5 6.1 - - - +
328A GLN* 1.3 75.9 - - - +
330A CYS* 1.3 63.9 + - - +
332A THR* 2.9 19.7 + - - +
333A TYR* 3.0 11.4 + - - +
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Residues in contact with CYS 330 (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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115A VAL* 4.2 3.4 - - + -
116A LYS* 3.8 29.8 - - - -
119A LEU* 3.6 29.4 - - + -
144A TRP* 3.6 13.5 - - - -
326A ASP 2.9 25.2 + - - +
327A TRP* 3.6 26.9 - - + -
329A VAL* 1.3 76.0 - - - +
331A ALA* 1.3 57.0 + - - +
333A TYR* 3.3 1.9 + - - +
334A LEU* 2.9 35.1 + - - +
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Residues in contact with ALA 331 (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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301A LEU* 3.7 30.3 - - + +
327A TRP* 2.8 40.3 + - + +
328A GLN* 3.9 7.9 - - - +
330A CYS* 1.3 70.9 - - - +
332A THR* 1.3 65.8 + - + +
334A LEU* 3.3 2.0 + - - -
335A ARG* 3.0 24.3 + - - +
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Residues in contact with THR 332 (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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151A LEU* 3.8 26.4 - - + +
156A VAL* 5.5 11.0 - - + -
328A GLN* 3.0 15.6 + - + +
329A VAL* 2.9 20.6 + - - +
331A ALA* 1.3 77.1 - - + +
333A TYR* 1.3 62.5 + - - +
335A ARG* 3.5 18.1 - - - +
336A THR* 4.5 2.8 + - - -
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Residues in contact with TYR 333 (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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119A LEU* 3.6 29.4 - - + -
165A LEU* 3.5 53.8 + - + -
166A GLU* 4.5 13.0 - - + -
168A LEU 4.5 1.6 + - - -
169A ARG* 5.3 2.3 + - - -
221A TYR* 3.4 31.0 - - - +
222A TYR 5.1 0.7 + - - -
329A VAL 3.0 18.6 + - - +
330A CYS* 3.6 4.9 - - - +
332A THR* 1.3 78.5 + - - +
334A LEU* 1.3 70.4 + - + +
335A ARG 3.1 1.3 + - - -
336A THR* 3.3 14.7 + - - -
337A ALA* 3.4 32.8 - - + +
339A VAL* 4.3 10.5 - - + -
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Residues in contact with LEU 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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115A VAL* 3.5 34.1 - - + -
248A PHE 4.6 1.1 - - - +
249A GLY* 4.3 11.0 - - - -
250A GLN* 3.0 16.1 + - - -
301A LEU* 3.8 14.1 - - + -
305A LEU* 3.8 28.0 - - + -
327A TRP* 4.6 7.9 - - + -
330A CYS 2.9 22.7 + - - +
331A ALA 3.3 0.6 + - - +
333A TYR* 1.3 78.3 - - + +
335A ARG* 1.3 66.0 + - - +
336A THR 3.0 4.0 + - - -
337A ALA* 3.4 22.6 + - + +
339A VAL* 4.0 28.5 - - + -
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Residues in contact with ARG 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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224A LEU* 5.1 0.7 - - - +
250A GLN* 3.3 18.3 + - - +
295A HIS* 3.3 39.0 + - + -
300A SER* 3.2 27.8 + - - +
301A LEU* 3.9 4.7 - - - +
331A ALA 3.0 12.9 + - - +
332A THR* 3.5 17.3 - - - +
333A TYR 3.1 0.8 - - - -
334A LEU* 1.3 77.3 - - - +
336A THR* 1.3 83.5 + - + +
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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