Contacts of the strand formed by residues 255 - 264 (chain A) in PDB entry 1KAS
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 ALA 255 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.3 10.3 - - - +
7A VAL* 2.8 27.9 + - + +
253A ILE* 3.4 7.4 - - - +
254A TYR* 1.3 83.2 - - - +
256A GLU* 1.3 65.1 + - - +
354A ILE* 4.3 22.7 - - + +
357A LEU* 4.6 10.1 - - + -
409A PHE* 4.8 2.5 - - + -
410A LYS 3.5 17.9 - - - +
411A LYS* 4.9 1.1 - - - -
412A ILE* 4.7 7.0 - - - +
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Residues in contact with GLU 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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4A ARG* 3.2 39.8 + - - +
5A VAL 3.2 19.5 + - - +
6A VAL* 4.1 5.6 - - + +
7A VAL* 5.3 0.2 - - - -
255A ALA* 1.3 78.1 - - - +
257A LEU* 1.3 64.1 + - - +
258A VAL* 3.4 24.4 + - + +
409A PHE* 3.4 9.8 - - - -
410A LYS* 3.0 43.6 + - + +
412A ILE* 3.1 29.5 - - + +
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Residues in contact with LEU 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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5A VAL* 2.9 32.5 + - + +
6A VAL* 4.5 1.0 - - - +
7A VAL* 5.0 1.2 - - - +
170A ILE* 3.8 31.0 - - + +
174A ALA* 3.5 29.2 - - + -
240A LEU* 4.1 15.0 - - + -
255A ALA 4.4 0.4 + - - -
256A GLU* 1.3 75.5 - - - +
258A VAL* 1.3 57.7 + - - +
259A GLY 3.4 28.0 - - - +
260A PHE* 4.9 2.7 - - + -
407A LEU* 3.5 15.3 - - + -
408A ILE 3.9 5.6 - - - +
409A PHE* 4.1 17.9 - - + -
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Residues in contact with VAL 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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256A GLU* 3.4 35.2 + - + +
257A LEU* 1.3 72.7 - - - +
259A GLY* 1.3 58.9 + - - +
289A ASP* 3.6 6.3 - - - +
290A ALA* 3.3 26.6 - - + +
392A TYR* 4.1 6.3 - - + -
408A ILE* 3.0 36.6 + - + +
410A LYS* 3.8 31.6 - - + -
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Residues in contact with GLY 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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257A LEU* 3.4 13.8 - - - +
258A VAL* 1.3 84.7 - - - +
260A PHE* 1.3 60.3 + - - +
286A ALA* 3.9 19.3 - - - -
289A ASP* 3.6 7.4 - - - -
290A ALA* 4.0 4.3 - - - -
407A LEU* 3.5 2.8 - - - -
408A ILE* 3.0 27.9 + - - -
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Residues in contact with PHE 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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167A VAL* 3.8 26.2 - - + -
168A HIS* 3.9 11.2 - - - -
171A GLY* 3.8 24.0 - - - +
172A HIS* 3.6 33.2 - + - -
175A ARG* 3.0 54.7 + - - +
257A LEU* 4.9 3.6 - - + -
259A GLY* 1.3 74.1 - - - +
261A GLY* 1.3 70.8 + - - +
262A MET* 3.5 26.4 - - + +
285A ASN* 4.4 1.0 - - - +
286A ALA* 3.9 4.6 - - - +
289A ASP* 2.8 19.1 + - - +
406A SER 3.5 10.3 - - - -
407A LEU* 3.7 13.9 - - + -
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Residues in contact with GLY 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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260A PHE* 1.3 76.1 - - - +
262A MET* 1.3 64.4 + - - +
282A ALA* 3.6 12.8 - - - -
285A ASN* 3.9 5.8 - - - -
286A ALA* 3.5 22.1 - - - +
405A GLY* 3.1 5.7 - - - -
406A SER 3.0 32.3 + - - +
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Residues in contact with MET 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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168A HIS* 3.8 16.4 - - + -
172A HIS* 3.3 34.5 - - + +
175A ARG* 4.8 10.5 - - - +
260A PHE* 3.5 31.0 - - + +
261A GLY* 1.3 72.6 - - - +
263A SER* 1.3 60.0 + - - +
282A ALA* 4.3 2.5 - - - -
285A ASN* 3.1 24.1 + - - +
404A ASN 3.3 7.2 - - - +
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Residues in contact with SER 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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262A MET* 1.3 78.3 - - - +
264A SER* 1.3 65.5 + - - +
278A GLY 2.6 28.7 + - - -
281A LEU* 3.9 18.8 - - - -
282A ALA 3.9 10.5 - - - -
402A GLY 3.7 0.3 - - - +
403A THR* 3.7 3.8 + - - -
404A ASN* 2.7 51.5 + - - +
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Residues in contact with SER 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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263A SER* 1.3 78.6 + - - +
265A ASP* 1.3 66.2 + - - +
266A ALA* 3.5 9.9 - - - +
278A GLY* 4.3 7.4 - - - -
281A LEU* 5.2 5.4 - - - +
401A GLY 5.5 1.8 - - - -
402A GLY 3.0 12.3 - - - -
403A THR* 5.1 1.6 - - - -
404A ASN* 4.0 1.3 - - - -
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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