Contacts of the helix formed by residues 251 - 265 (chain A) in PDB entry 1K30
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 ASP 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS* 4.6 19.3 + - - +
231A PRO* 3.0 23.3 + - - +
232A SER* 5.4 1.3 - - - +
250A PHE* 1.3 75.7 - - - +
252A ALA* 1.3 64.1 + - - +
253A SER* 2.9 23.9 + - - -
254A SER* 2.9 32.1 + - - +
255A VAL* 3.5 3.6 + - - +
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Residues in contact with ALA 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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250A PHE 3.6 5.7 + - - -
251A ASP* 1.3 72.2 + - - +
253A SER* 1.3 62.2 + - - +
255A VAL* 3.4 4.2 + - - +
256A ASP* 3.1 22.0 + - - +
327A ARG* 4.0 15.5 - - + +
328A GLU* 3.4 32.5 - - - +
331A SER* 3.5 31.5 + - - -
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Residues in contact with SER 253 (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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251A ASP* 2.9 16.5 + - - -
252A ALA* 1.3 78.2 - - - +
254A SER* 1.3 58.1 + - - +
256A ASP* 3.2 7.1 + - - +
257A ASN* 2.8 43.6 + - - +
327A ARG* 5.4 6.2 + - - +
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Residues in contact with SER 254 (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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229A ILE* 4.8 12.3 - - - +
231A PRO* 4.1 22.0 + - - -
251A ASP* 2.9 26.3 + - - +
253A SER* 1.3 74.3 - - - +
255A VAL* 1.3 66.9 - - - +
257A ASN* 3.9 8.1 - - - +
258A MET* 3.2 27.9 + - - +
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Residues in contact with VAL 255 (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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136A ILE* 4.3 14.1 - - + -
231A PRO* 3.6 31.0 - - + -
250A PHE* 4.1 6.5 - - + -
251A ASP 3.5 1.4 + - - +
252A ALA 3.4 7.7 + - - +
253A SER 3.3 0.4 - - - -
254A SER* 1.3 74.5 - - - +
256A ASP* 1.3 63.6 + - - +
258A MET* 3.2 7.7 + - - +
259A ARG* 3.0 20.1 + - - +
271A LEU* 4.5 5.5 - - + +
327A ARG 5.7 0.4 - - - +
330A TYR* 3.8 22.0 - - + -
331A SER* 3.9 23.8 - - - +
334A LEU* 3.6 25.1 - - + -
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Residues in contact with ASP 256 (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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252A ALA 3.1 18.1 + - - +
253A SER* 3.6 5.6 - - - +
255A VAL* 1.3 79.8 - - - +
257A ASN* 1.3 58.4 + - - +
259A ARG* 3.0 35.4 + - - +
260A ARG* 2.7 60.5 + - - +
327A ARG* 3.4 42.0 + - + +
330A TYR* 5.8 1.3 - - - -
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Residues in contact with ASN 257 (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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213A LEU* 5.9 11.2 - - + +
253A SER* 2.8 34.6 + - - +
254A SER* 3.9 8.1 + - - +
256A ASP* 1.3 73.9 - - - +
258A MET* 1.3 62.6 + - + +
260A ARG* 2.9 29.9 + - - +
261A LEU* 3.0 33.1 + - + +
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Residues in contact with MET 258 (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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134A VAL* 3.8 35.9 - - + -
136A ILE* 5.2 4.9 - - + -
166A VAL* 5.2 1.3 - - - -
216A MET* 4.0 35.4 - - + +
220A LEU* 5.0 7.4 - - + -
227A ILE* 4.7 9.6 - - + -
229A ILE* 3.8 34.8 - - + -
254A SER 3.2 12.5 + - - +
255A VAL* 3.2 9.2 + - - +
257A ASN* 1.3 79.8 - - + +
259A ARG* 1.3 62.4 + - - +
261A LEU* 3.2 11.8 + - + +
262A ILE* 3.1 28.3 + - + +
271A LEU* 5.3 1.8 - - + -
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Residues in contact with ARG 259 (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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255A VAL 3.0 13.4 + - - +
256A ASP* 3.0 32.2 + - - +
258A MET* 1.3 75.0 - - - +
260A ARG* 1.3 74.9 + - - +
262A ILE* 3.3 12.4 + - + +
263A GLN* 3.0 47.3 + - + +
271A LEU* 4.3 16.9 - - + +
313A PHE* 3.3 62.6 - - + -
326A VAL* 5.7 1.0 - - - +
327A ARG* 5.4 1.0 - - - +
330A TYR* 3.7 17.0 - - + +
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Residues in contact with ARG 260 (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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256A ASP* 2.7 34.3 + - - +
257A ASN* 2.9 31.7 + - - +
259A ARG* 1.3 101.7 - - - +
261A LEU* 1.3 59.7 + - - +
263A GLN* 3.2 15.0 + - - +
264A HIS* 2.8 49.4 + - + -
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Residues in contact with LEU 261 (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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213A LEU* 4.3 29.4 - - + +
216A MET* 3.9 33.4 - - + -
217A ALA* 4.3 23.1 - - + +
220A LEU* 4.2 14.7 - - + +
257A ASN* 3.0 22.1 + - + +
258A MET* 3.6 14.8 - - - +
260A ARG* 1.3 72.2 - - - +
262A ILE* 1.3 65.4 + - - +
264A HIS* 3.4 8.6 + - + +
265A SER* 3.0 24.6 + - - -
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Residues in contact with ILE 262 (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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132A ASN* 5.3 4.5 - - + +
134A VAL* 3.5 21.1 - - + -
220A LEU* 4.3 18.6 - - + -
258A MET* 3.1 15.3 + - + +
259A ARG* 3.3 10.8 - - + +
261A LEU* 1.3 74.5 - - - +
263A GLN* 1.3 64.2 + - - +
265A SER* 2.5 27.1 + - - +
266A ASP 3.9 1.6 + - - -
267A VAL 4.0 5.8 - - - +
269A GLY* 3.6 39.3 - - - +
270A HIS 4.6 0.2 - - - +
271A LEU* 3.3 35.0 - - + -
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Residues in contact with GLN 263 (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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259A ARG* 3.0 34.0 + - + +
260A ARG* 3.2 18.7 + - - +
262A ILE* 1.3 78.9 - - - +
264A HIS* 1.3 72.1 + - + +
265A SER 3.5 0.2 + - - -
266A ASP* 3.7 14.0 + - - +
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Residues in contact with HIS 264 (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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221A ARG* 3.0 18.0 + - - -
260A ARG* 2.8 49.6 + - + +
261A LEU* 3.8 9.0 + - + +
262A ILE 3.3 0.2 - - - -
263A GLN* 1.3 83.2 + - + +
265A SER* 1.3 60.2 + - - +
266A ASP* 3.2 9.6 + - - +
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Residues in contact with SER 265 (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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132A ASN* 4.5 2.3 + - - -
217A ALA* 4.8 2.5 - - - -
220A LEU* 3.8 27.8 - - - +
221A ARG* 3.5 31.3 + - - +
261A LEU 3.0 14.3 + - - -
262A ILE* 2.5 22.1 + - - +
264A HIS* 1.3 75.1 - - - +
266A ASP* 1.3 68.4 + - - +
267A VAL* 3.2 24.5 + - - +
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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