Contacts of the helix formed by residues 307 - 324 (chain A) in PDB entry 1K1S
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 307 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274A TYR* 5.0 0.2 - - - -
280A ILE* 5.2 6.8 - - - +
305A GLY 3.7 5.3 + - - -
306A ILE* 1.3 76.8 - - - +
308A ILE* 1.3 59.5 + - - +
309A ASP* 2.8 23.8 - - - -
310A ASN* 3.0 21.1 + - - +
311A ALA* 2.8 24.9 + - - +
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Residues in contact with ILE 308 (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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270A ILE* 3.3 33.4 - - + +
271A ASN* 4.0 11.9 - - - +
274A TYR* 3.5 37.3 - - + -
306A ILE 3.7 0.6 + - - -
307A SER* 1.3 72.5 - - - +
309A ASP* 1.3 71.1 + - + +
311A ALA* 3.2 17.8 + - - +
312A TYR* 3.2 32.7 + - + +
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Residues in contact with ASP 309 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307A SER* 2.8 24.6 - - - -
308A ILE* 1.3 84.0 - - + +
310A ASN* 1.3 75.5 + - - +
312A TYR* 3.6 21.3 + - + +
313A LYS* 3.7 11.6 + - - +
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Residues in contact with ASN 310 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A PHE* 6.2 1.8 - - + -
306A ILE* 4.0 12.6 - - + -
307A SER* 3.0 38.1 + - - +
309A ASP* 1.3 87.1 + - - +
311A ALA* 1.3 61.1 + - - +
313A LYS* 3.1 7.0 + - - +
314A VAL* 2.8 40.5 + - + +
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Residues in contact with ALA 311 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270A ILE* 3.5 24.4 - - + +
274A TYR* 3.6 18.4 - - + +
284A ILE* 3.9 20.3 - - + +
306A ILE* 4.0 0.4 - - - +
307A SER 2.8 12.8 + - - +
308A ILE* 3.2 12.8 - - - +
310A ASN* 1.3 78.3 - - - +
312A TYR* 1.3 57.0 + - - +
314A VAL* 4.1 0.2 - - - +
315A ALA* 2.8 35.2 + - - +
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Residues in contact with TYR 312 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263A LEU* 5.1 3.6 - - - +
267A LYS* 3.9 56.2 - - + +
270A ILE* 3.9 23.3 - - + -
271A ASN* 2.4 34.6 + - - -
308A ILE* 3.2 29.6 + - + +
309A ASP* 3.8 14.8 - - + +
310A ASN 3.2 0.4 - - - -
311A ALA* 1.3 75.5 - - - +
313A LYS* 1.3 63.5 + - - +
315A ALA* 3.9 1.2 - - - +
316A GLU* 3.0 24.6 + - - +
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Residues in contact with LYS 313 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A LYS* 6.0 1.6 - - - +
309A ASP 3.7 8.8 + - - +
310A ASN* 3.1 10.4 + - - +
312A TYR* 1.3 77.8 - - - +
314A VAL* 1.3 74.6 + - + +
316A GLU* 3.2 19.7 + - - +
317A ASP* 2.7 41.6 + - - +
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Residues in contact with VAL 314 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 4.8 10.1 - - + -
300A LYS* 4.2 21.5 + - + +
302A PHE* 3.8 31.2 - - + -
306A ILE* 5.1 3.6 - - + -
310A ASN* 2.8 30.5 + - + +
311A ALA* 4.1 4.3 - - - +
313A LYS* 1.3 82.9 - - + +
315A ALA* 1.3 62.6 + - - +
317A ASP* 3.2 8.0 + - + +
318A LEU* 3.0 44.2 + - + +
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Residues in contact with ALA 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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266A LEU* 3.7 14.9 - - + +
270A ILE* 3.4 23.8 - - + -
284A ILE* 5.2 6.2 - - + +
286A VAL* 3.7 19.8 - - + +
311A ALA 2.8 25.3 + - - +
312A TYR 3.9 2.2 - - - +
314A VAL* 1.3 75.4 - - - +
316A GLU* 1.3 56.6 + - - +
318A LEU* 3.1 5.1 + - - +
319A LEU* 2.9 29.3 + - - +
336A VAL* 5.8 0.2 - - + -
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Residues in contact with GLU 316 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 5.1 2.5 - - + -
263A LEU* 3.2 42.4 - - + +
266A LEU* 4.4 0.4 - - - +
267A LYS* 6.2 0.7 - - - -
312A TYR 3.0 18.4 + - - +
313A LYS* 3.5 10.5 - - - +
315A ALA* 1.3 76.8 - - - +
317A ASP* 1.3 62.3 + - - +
319A LEU* 3.2 8.4 + - + +
320A ARG* 2.9 61.6 + - + +
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Residues in contact with ASP 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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300A LYS* 5.3 11.0 - - - +
313A LYS* 2.7 52.0 + - - +
314A VAL* 3.2 6.7 + - - +
316A GLU* 1.3 77.3 - - - +
318A LEU* 1.3 66.3 + - + +
320A ARG* 3.2 12.3 + - - +
321A GLU* 3.0 32.1 + - + +
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Residues in contact with LEU 318 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A ILE* 3.9 23.6 - - + +
286A VAL* 3.4 29.6 - - + -
298A LYS* 3.9 37.4 - - + +
299A GLY* 4.1 9.4 - - - +
300A LYS* 3.9 23.3 - - + -
314A VAL* 3.0 32.7 + - + +
315A ALA* 3.1 7.6 + - - +
317A ASP* 1.3 77.6 - - + +
319A LEU* 1.3 61.6 + - - +
321A GLU* 3.5 7.5 + - - +
322A LEU* 3.2 29.8 + - - +
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Residues in contact with LEU 319 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 3.8 25.6 - - + -
262A ILE* 4.0 18.8 - - + -
263A LEU* 5.6 3.4 - - + +
266A LEU* 3.8 17.3 - - + -
286A VAL* 4.6 8.2 - - + +
288A ALA* 5.5 3.6 - - + -
315A ALA 2.9 13.1 + - - +
316A GLU* 3.4 10.5 - - - +
318A LEU* 1.3 75.1 - - - +
320A ARG* 1.3 70.6 + - - +
322A LEU* 3.4 9.8 + - + +
323A LEU* 3.2 42.8 + - + +
331A VAL* 5.4 5.6 - - + -
334A ILE* 3.7 22.9 - - + -
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Residues in contact with ARG 320 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A VAL* 3.6 38.7 - - - +
316A GLU* 2.9 56.3 + - + +
317A ASP* 3.2 13.7 + - - +
319A LEU* 1.3 77.8 - - - +
321A GLU* 1.3 65.8 + - + +
323A LEU* 2.8 18.4 + - - +
324A VAL* 2.9 20.9 + - + +
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Residues in contact with GLU 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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298A LYS* 2.9 46.6 + - + +
300A LYS* 4.6 8.0 + - - -
317A ASP* 3.0 19.6 + - + +
318A LEU* 3.7 11.3 - - - +
319A LEU 3.4 0.2 - - - -
320A ARG* 1.3 79.4 - - + +
322A LEU* 1.3 55.4 + - - +
324A VAL* 2.7 31.2 + - - +
325A ARG* 3.0 15.1 + - - +
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Residues in contact with LEU 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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286A VAL* 3.7 28.5 - - + +
288A ALA* 4.2 14.8 - - + -
296A LEU* 3.5 34.0 - - + +
297A SER* 3.8 11.4 - - - -
298A LYS* 4.0 8.7 - - + +
318A LEU 3.2 19.7 + - - +
319A LEU* 3.7 9.6 - - + +
320A ARG 3.3 0.2 - - - -
321A GLU* 1.3 78.4 - - - +
323A LEU* 1.3 58.8 + - + +
325A ARG* 3.0 41.9 + - - +
326A ASP* 3.1 30.3 + - - +
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Residues in contact with LEU 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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257A ARG* 3.6 52.9 + - + +
259A VAL* 3.8 18.2 - - + -
262A ILE* 4.6 2.2 - - + -
319A LEU* 3.2 40.8 + - + +
320A ARG* 2.8 11.2 + - - +
322A LEU* 1.3 74.8 - - + +
324A VAL* 1.3 58.6 + - + +
325A ARG 3.1 5.9 + - - -
326A ASP* 3.2 18.6 - - - +
327A LYS* 3.9 7.3 - - - +
329A ARG 5.3 0.9 - - - +
331A VAL* 4.3 20.0 - - + -
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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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320A ARG* 3.1 22.7 - - + +
321A GLU* 2.7 12.6 + - - +
323A LEU* 1.3 78.0 - - + +
325A ARG* 1.3 56.1 + - - +
327A LYS* 3.9 16.0 + - - +
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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