Contacts of the helix formed by residues 309 - 321 (chain A) in PDB entry 2KSB
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 ASN 309 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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245A LYS* 5.8 8.5 - - + +
246A VAL* 6.4 3.1 - - + -
249A MET* 3.3 32.0 - - + +
305A TYR* 2.8 22.1 + - - +
306A CYS 3.7 3.0 - - - +
307A CYS 3.5 1.7 - - - -
308A LEU* 1.3 77.3 - - + +
310A ASP* 1.3 65.8 + - - +
311A ARG* 4.3 6.1 - - + +
312A PHE* 2.7 52.4 + - - +
313A ARG* 3.0 15.6 + - - +
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Residues in contact with ASP 310 (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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245A LYS* 5.1 10.1 - - - +
309A ASN* 1.3 73.0 - - - +
311A ARG* 1.3 62.6 + - - +
313A ARG* 2.9 31.5 + - - +
314A LEU* 2.7 45.3 + - + +
331A TYR* 2.8 48.9 + - - +
332A GLU* 4.7 4.0 - - - +
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Residues in contact with ARG 311 (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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62A ARG* 3.1 56.0 - - - +
63A MET* 4.3 21.9 - - + +
65A THR* 4.4 11.5 - - - +
68A ASN* 5.6 0.6 - - - +
242A ALA* 4.6 15.6 + - - +
243A LYS* 5.9 4.0 - - - +
246A VAL* 5.5 12.7 - - - +
309A ASN* 3.2 6.9 - - + +
310A ASP* 1.3 82.4 + - - +
312A PHE* 1.3 64.9 + - + +
314A LEU* 3.5 1.4 + - - +
315A GLY 2.9 18.4 + - - -
331A TYR* 2.9 34.4 + - + +
334A LEU* 3.7 19.2 + - - +
335A GLU* 4.1 7.2 - - - +
341A TYR* 3.2 8.4 + - - +
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Residues in contact with PHE 312 (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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53A VAL* 4.5 7.0 - - + -
56A ILE* 4.2 3.1 - - + -
57A ILE* 3.3 22.2 - - + -
63A MET* 2.9 37.2 - - + -
68A ASN* 4.0 11.7 - - - -
71A LEU* 4.2 7.9 - - + -
305A TYR* 3.8 28.3 - + - +
309A ASN* 2.7 44.3 + - - +
311A ARG* 1.3 74.6 - - + +
313A ARG* 1.3 55.8 + - - +
316A PHE* 2.6 79.0 + + + -
341A TYR* 4.0 5.6 - - - -
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Residues in contact with ARG 313 (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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306A CYS* 4.0 24.0 + - + +
307A CYS 5.8 1.6 + - - -
309A ASN 3.0 15.0 + - - +
310A ASP* 2.9 31.4 + - - +
312A PHE* 1.3 78.8 - - - +
314A LEU* 1.3 80.2 + - + +
316A PHE* 3.7 9.0 - - - +
317A LYS* 3.2 38.4 + - - +
328A ALA* 5.5 4.2 + - - +
330A ASP 5.2 1.8 + - - -
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Residues in contact with LEU 314 (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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310A ASP* 2.7 40.8 + - + +
311A ARG 4.1 2.0 - - - +
313A ARG* 1.3 101.6 - - - +
315A GLY* 1.3 65.4 + - - +
317A LYS* 3.3 16.1 + - - +
318A HIS* 3.0 14.1 + - + -
326A ILE* 2.7 38.3 - - + +
327A SER 4.0 5.8 - - - +
328A ALA* 4.4 7.0 - - + +
330A ASP* 3.1 44.6 - - - +
331A TYR* 3.4 11.9 - - + +
335A GLU* 5.3 0.4 - - + -
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Residues in contact with GLY 315 (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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56A ILE* 3.3 5.8 - - - -
60A HIS* 2.8 24.7 + - - -
311A ARG 2.9 10.9 + - - -
314A LEU* 1.3 76.2 - - - +
316A PHE* 1.4 61.6 + - - +
318A HIS* 3.0 10.8 + - - +
319A ALA 3.2 0.2 + - - -
341A TYR* 2.8 38.5 - - - -
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Residues in contact with PHE 316 (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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52A VAL* 3.1 37.4 - - + +
53A VAL* 4.2 15.5 - - + -
56A ILE* 2.9 44.9 - - + +
302A PRO 5.8 0.2 - - - -
305A TYR* 4.4 11.9 - - + -
306A CYS* 4.4 18.2 - - - -
312A PHE* 2.6 68.9 + + + +
313A ARG* 3.7 8.7 - - - +
315A GLY* 1.4 67.9 - - - +
317A LYS* 1.3 55.0 + - - +
319A ALA* 2.7 25.8 + - + +
320A PHE* 2.8 16.4 + - - +
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Residues in contact with LYS 317 (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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313A ARG* 3.2 30.2 + - - +
314A LEU* 3.4 19.0 - - - +
316A PHE* 1.3 76.4 - - - +
318A HIS* 1.3 66.7 + - - +
320A PHE* 3.7 8.9 - - + +
321A ARG* 3.0 32.9 + - + +
324A PRO 4.4 1.3 - - - +
325A PHE 4.9 11.2 - - - +
326A ILE* 4.7 12.3 - - + -
327A SER 4.9 2.0 - - - +
328A ALA* 3.6 28.0 - - + +
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Residues in contact with HIS 318 (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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60A HIS* 3.7 14.3 - + + -
314A LEU 3.0 9.3 + - - -
315A GLY* 3.0 29.9 - - - +
316A PHE 3.1 0.2 - - - -
317A LYS* 1.3 78.4 - - - +
319A ALA* 1.3 53.6 + - - +
321A ARG 2.5 26.2 - - - +
322A CYS 4.2 2.8 - - - +
323A CYS 3.2 6.6 - - - +
324A PRO* 3.9 10.1 - - + -
326A ILE* 2.9 55.6 - - + +
330A ASP* 3.9 0.4 + - - -
335A GLU* 4.3 11.4 - - + -
340A ARG* 3.8 15.7 - - + +
341A TYR* 4.0 20.6 - + - -
342A LEU* 4.6 2.5 - - + +
345A GLN* 3.9 25.6 + - - +
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Residues in contact with ALA 319 (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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52A VAL* 6.1 2.5 - - + -
55A TRP* 4.6 22.2 - - + +
56A ILE* 5.1 4.5 - - + -
59A ALA* 5.9 0.4 - - + -
60A HIS* 4.1 16.5 + - + +
315A GLY 3.2 1.4 + - - -
316A PHE* 2.7 18.7 + - + +
318A HIS* 1.3 78.6 - - - +
320A PHE* 1.4 65.7 + - - +
321A ARG 3.3 5.5 - - - +
322A CYS* 4.1 5.1 + - - +
342A LEU* 4.8 6.3 - - + -
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Residues in contact with PHE 320 (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 PHE 2.8 14.2 + - - +
317A LYS* 3.1 13.6 + - + +
319A ALA* 1.4 74.5 - - - +
321A ARG* 1.3 75.4 + - + +
322A CYS* 3.2 3.5 + - - -
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Residues in contact with ARG 321 (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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317A LYS* 3.0 16.2 + - + +
318A HIS 2.5 27.4 - - - +
319A ALA 3.3 0.9 - - - +
320A PHE* 1.3 89.5 - - + +
322A CYS* 1.3 58.4 + - - +
323A CYS 2.5 18.2 - - - +
324A PRO 4.0 3.4 - - - +
325A PHE* 3.0 56.5 + - + +
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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