Contacts of the helix formed by residues 321 - 335 (chain A) in PDB entry 4K2S
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 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.5 28.9 - - - -
21A THR* 5.1 1.4 + - - -
35A ASP* 3.0 32.9 + - - -
37A THR* 4.4 0.2 - - - -
320A LEU* 1.3 76.9 - - - +
322A PRO* 1.3 75.1 - - - +
323A VAL* 3.1 21.8 + - - +
324A CYS* 2.9 11.6 + - - +
325A LEU* 3.0 10.4 + - - +
346A HIS* 3.8 1.1 - - - -
354A PHE* 4.4 8.6 - - - -
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Residues in contact with PRO 322 (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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19A PHE* 4.7 0.4 - - + -
321A SER* 1.3 88.3 - - - +
323A VAL* 1.3 56.5 + - - +
325A LEU* 3.6 5.2 - - + -
326A GLY 2.9 24.1 + - - -
346A HIS* 3.7 18.2 - - + +
350A THR* 3.7 23.8 - - + +
351A ASP* 4.5 5.4 - - - +
354A PHE* 3.5 43.1 - - + +
356A HIS* 4.6 0.4 - - - +
358A TYR* 3.4 23.8 - - + +
375A VAL* 3.4 12.8 - - + +
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Residues in contact with VAL 323 (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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21A THR* 4.5 6.7 - - + -
33A ILE* 3.7 27.6 - - + +
34A GLY* 3.8 2.0 - - - -
35A ASP* 3.6 22.9 - - + +
93A MET* 4.5 3.1 - - - -
321A SER* 3.0 13.2 - - - +
322A PRO* 1.3 75.6 - - - +
324A CYS* 1.3 65.9 + - - +
326A GLY* 3.6 0.5 + - - -
327A ALA* 3.1 22.9 + - - +
354A PHE* 3.6 28.7 - - + -
373A HIS* 3.7 26.2 - - + +
375A VAL* 3.9 11.2 - - + +
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Residues in contact with CYS 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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35A ASP* 3.5 8.4 - - + +
93A MET* 4.2 9.4 - - - -
288A PRO* 4.6 1.3 - - - -
289A LEU* 4.0 15.4 - - - +
290A THR* 3.0 42.4 - - - +
315A HIS 5.6 0.7 - - - -
320A LEU* 4.0 23.8 - - + -
321A SER* 2.9 11.0 + - - +
323A VAL* 1.3 80.0 - - - +
325A LEU* 1.3 52.4 + - - +
327A ALA* 3.3 1.6 + - - +
328A ALA* 2.7 41.4 + - - +
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Residues in contact with LEU 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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316A GLY* 5.9 4.9 - - - +
320A LEU* 5.5 1.1 - - + +
321A SER 3.0 11.8 + - - +
322A PRO* 3.7 10.5 - - + +
324A CYS* 1.3 77.9 - - - +
326A GLY* 1.3 58.1 + - - +
328A ALA* 3.2 3.6 + - + +
329A ILE* 2.8 53.1 + - + +
341A GLN* 4.2 17.7 - - - +
342A GLU 5.0 2.7 - - - +
343A HIS* 5.2 5.6 - - + -
344A MET 5.8 2.2 - - - +
345A PRO* 6.5 0.2 - - + -
346A HIS* 4.3 17.9 - - + +
358A TYR* 3.6 27.4 - - + +
365A PHE* 3.9 26.7 - - + -
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Residues in contact with GLY 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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322A PRO 2.9 18.3 + - - -
325A LEU* 1.3 72.9 - - - +
327A ALA* 1.3 60.9 + - - +
329A ILE* 3.3 4.4 + - - +
330A HIS* 3.2 27.2 + - - -
358A TYR* 3.5 26.3 - - - +
373A HIS 4.1 8.5 - - - -
375A VAL* 3.8 9.4 - - - -
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Residues in contact with ALA 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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93A MET* 4.2 17.7 - - + -
107A LEU* 4.4 13.2 - - + +
289A LEU* 3.5 18.6 - - + +
295A ILE* 4.4 1.3 - - + +
323A VAL 3.1 17.4 + - - +
324A CYS 3.8 1.1 - - - +
326A GLY* 1.3 75.0 - - - +
328A ALA* 1.3 58.4 - - - +
330A HIS* 3.3 4.7 + - - +
331A PHE* 3.0 27.0 + - - +
373A HIS* 4.0 23.3 - - + +
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Residues in contact with ALA 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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289A LEU* 3.5 13.6 - - + +
314A PHE* 3.9 21.5 - - + -
324A CYS* 2.7 27.3 + - - +
325A LEU* 3.5 7.4 - - + +
327A ALA* 1.3 72.2 - - - +
329A ILE* 1.3 56.1 + - - +
331A PHE* 3.2 3.7 + - - +
332A ASP* 2.7 41.6 + - - +
341A GLN* 4.1 13.0 - - - +
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Residues in contact with ILE 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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119A VAL* 4.5 4.3 - - + -
325A LEU* 2.8 33.5 + - + +
326A GLY* 3.8 4.3 - - - +
327A ALA 3.3 0.4 - - - -
328A ALA* 1.3 77.4 - - - +
330A HIS* 1.3 60.8 + - + +
332A ASP* 3.4 11.2 + - - +
333A THR* 2.8 31.3 + - - +
341A GLN* 5.2 0.7 - - + -
358A TYR* 3.6 26.9 - - + -
365A PHE* 3.5 48.5 - - + -
366A LEU 4.0 4.9 - - - +
367A ALA* 3.6 33.0 - - + +
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Residues in contact with HIS 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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106A PRO* 3.6 18.8 - - + -
107A LEU* 3.6 22.2 - - + -
108A TYR* 3.1 34.6 + + - +
111A LEU* 4.4 2.0 - - - -
326A GLY 3.2 18.1 + - - -
327A ALA 3.5 7.6 - - - +
329A ILE* 1.3 76.6 - - + +
331A PHE* 1.3 62.9 + - - +
333A THR* 3.1 14.6 + - - -
334A TRP* 3.2 10.7 + - - +
367A ALA* 4.1 1.9 - - + +
368A GLY* 3.3 40.4 + - - -
370A SER 5.0 0.4 + - - -
372A GLY 3.8 1.0 + - - -
373A HIS* 3.2 44.2 + - + -
374A GLY* 4.4 0.8 + - - -
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Residues in contact with PHE 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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111A LEU* 3.9 14.9 - - + +
289A LEU* 4.2 5.2 - - + -
295A ILE* 4.0 28.7 - - + -
298A MET* 3.6 27.6 - - + -
299A ARG* 3.6 24.0 - - + -
302A ALA* 3.9 8.5 - - + -
312A THR* 4.5 3.4 - - + -
314A PHE* 3.4 32.3 - + + -
327A ALA 3.0 13.8 + - - +
328A ALA* 3.2 8.7 + - - +
330A HIS* 1.3 73.5 - - - +
332A ASP* 1.3 59.8 + - - +
334A TRP* 3.2 21.3 + + - -
335A VAL* 2.8 53.3 + - + +
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Residues in contact with ASP 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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116A ARG* 2.7 36.2 + - - -
119A VAL* 3.6 14.1 - - + +
312A THR* 4.4 3.6 + - - -
314A PHE* 3.3 23.7 - - - -
328A ALA 2.7 26.1 + - - +
329A ILE* 3.5 7.5 - - - +
331A PHE* 1.3 74.1 - - - +
333A THR* 1.3 53.4 + - - +
335A VAL* 4.0 4.2 + - - -
338A PHE* 3.4 33.4 - - + +
340A ILE 5.0 0.5 - - - +
341A GLN* 2.5 35.9 + - - +
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Residues in contact with THR 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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108A TYR* 4.0 18.4 - - + -
114A LYS* 3.5 28.9 - - + -
115A SER 2.8 29.3 + - - -
116A ARG* 3.5 25.0 + - - +
118A ARG* 6.0 0.2 - - - -
119A VAL* 3.6 13.1 - - - +
329A ILE 2.8 19.3 + - - -
330A HIS 3.1 6.7 + - - -
332A ASP* 1.3 78.9 - - - +
334A TRP* 1.3 53.0 + - - +
367A ALA* 3.4 20.2 + - + +
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Residues in contact with TRP 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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108A TYR* 4.1 5.4 - - + +
111A LEU* 3.3 47.5 + - + -
112A GLY* 3.8 11.8 + - - -
113A GLY 3.4 24.9 - - - +
115A SER* 2.6 25.1 + - - +
299A ARG* 3.9 36.8 - - + -
303A ASP* 4.2 13.5 - - - -
330A HIS 3.2 9.8 + - - +
331A PHE* 3.2 30.3 + + - +
333A THR* 1.3 79.2 - - - +
335A VAL* 1.3 96.7 + - + +
336A PRO* 3.2 15.6 - - + +
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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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116A ARG* 2.7 26.7 + - - -
302A ALA* 3.8 22.2 - - + -
303A ASP* 5.4 0.9 - - - +
312A THR* 4.1 8.1 - - + +
331A PHE* 2.8 36.5 + - + +
332A ASP* 4.0 6.1 - - - +
333A THR 3.8 0.6 - - - -
334A TRP* 1.3 89.8 - - + +
336A PRO* 1.3 73.5 - - + +
337A ASN* 3.3 23.6 - - - +
338A PHE* 3.5 24.0 + - + +
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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