Contacts of the strand formed by residues 246 - 251 (chain A) in PDB entry 1KYO
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 246 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A THR* 2.9 31.5 + - - -
167A ALA* 4.3 0.5 + - - -
169A GLN* 3.4 12.7 + - - -
244A LEU* 2.8 18.5 + - - +
245A GLY* 1.3 75.0 - - - -
247A GLU* 1.3 64.5 + - - +
430A ILE 3.5 5.7 + - - +
431A ALA* 3.2 6.6 - - - +
432A ILE 3.1 21.0 + - - -
444A TYR* 3.8 6.6 + - - -
28H ALA 3.2 17.0 - - - -
29H VAL* 4.1 6.5 - - - +
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Residues in contact with GLU 247 (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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166A THR* 3.6 7.4 + - - -
246A SER* 1.3 80.8 - - - +
248A VAL* 1.3 61.2 + - - +
249A ARG* 2.6 47.6 + - + +
432A ILE* 3.2 26.7 - - + +
444A TYR* 3.2 34.6 + - + +
298D ARG* 5.7 2.9 - - - -
26H SER* 3.7 2.9 + - - +
27H TYR* 3.3 7.3 - - - +
28H ALA* 3.0 49.6 + - + +
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Residues in contact with VAL 248 (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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162A HIS* 3.8 38.4 - - + +
166A THR* 3.9 14.8 - - + -
247A GLU* 1.3 74.7 - - - +
249A ARG* 1.3 65.0 + - - +
250A LEU* 3.9 24.7 + - + +
432A ILE 3.1 2.9 + - - +
433A ALA* 3.3 15.5 - - + -
434A GLY 3.3 18.2 + - - -
33E THR 4.9 0.2 - - - +
25H THR* 4.1 7.6 - - + -
26H SER 3.3 4.3 - - - +
27H TYR* 4.0 26.5 - - + +
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Residues in contact with ARG 249 (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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247A GLU* 2.6 52.2 + - + +
248A VAL* 1.3 77.3 - - - +
250A LEU* 1.3 58.2 + - - +
251A ARG* 3.1 12.3 + - + +
432A ILE* 4.8 7.0 - - + +
434A GLY 3.9 4.0 - - - +
438A ILE* 4.0 17.3 + - + +
441A LEU* 2.8 49.9 + - + +
442A LEU 2.7 31.1 + - - -
443A ASP* 4.4 2.1 - - - +
444A TYR* 4.0 4.8 - - - +
447A ILE* 4.6 0.2 - - - +
24H ILE 4.1 1.0 - - - +
25H THR* 3.7 3.9 - - - -
26H SER* 2.9 44.9 + - - +
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Residues in contact with LEU 250 (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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158A ARG* 4.4 17.7 + - + +
159A VAL* 5.6 3.1 - - + -
162A HIS* 3.5 43.5 - - + +
248A VAL* 3.9 10.5 - - + -
249A ARG* 1.3 68.9 - - - +
251A ARG* 1.3 65.1 + - - +
252A ASP* 4.1 1.7 - - - +
434A GLY 2.7 23.7 + - - +
435A THR* 2.9 30.0 + - - +
33E THR* 3.6 22.2 - - + +
24H ILE 4.7 2.5 - - - -
25H THR* 3.4 30.3 - - + +
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Residues in contact with ARG 251 (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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249A ARG* 3.1 9.6 + - + +
250A LEU* 1.3 75.9 - - - +
252A ASP* 1.3 60.1 + - - +
253A ASP* 2.6 54.9 + - - -
436A GLY 3.7 5.8 - - - +
438A ILE* 3.5 29.1 - - + +
439A GLU* 3.2 52.7 + - - +
215C ASN 5.0 0.4 + - - -
216C LEU 4.2 6.9 + - - -
19H PRO 5.1 0.8 + - - -
21H GLN* 3.2 50.4 + - + +
22H LYS* 4.2 7.3 - - - -
23H GLY 4.2 3.1 + - - -
24H ILE* 3.9 16.5 + - + +
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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