Contacts of the strand formed by residues 24 - 29 (chain H) 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 ILE 24 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A ARG 4.1 5.7 - - - +
250A LEU 4.7 0.7 - - - -
251A ARG* 3.9 20.8 + - + +
300D PHE* 3.7 31.4 - - + -
301D VAL 3.7 4.9 - - - +
302D PHE* 3.9 11.2 - - + -
69G TYR 4.0 13.7 - - - +
72G ALA* 4.5 6.7 - - + -
73G TYR* 3.8 37.7 - - + +
76G ILE* 4.4 14.4 - - + -
21H GLN* 4.8 12.3 - - + +
22H LYS 3.3 25.3 - - - +
23H GLY* 1.3 75.6 - - - +
25H THR* 1.3 64.2 + - - +
26H SER* 5.6 0.4 - - - -
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Residues in contact with THR 25 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248A VAL* 4.1 7.6 - - + -
249A ARG 3.7 5.4 - - - +
250A LEU* 3.4 37.2 - - + +
299D LYS 4.0 0.2 - - - +
300D PHE* 3.5 2.6 - - - +
301D VAL* 2.9 45.7 + - - +
303D ASN* 4.5 1.7 + - - -
33E THR* 3.8 18.9 - - + +
23H GLY 3.4 10.2 + - - -
24H ILE* 1.3 79.9 + - - +
26H SER* 1.3 64.1 + - - +
27H TYR* 4.0 15.8 - - + +
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Residues in contact with SER 26 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247A GLU* 3.7 3.5 + - - +
248A VAL* 3.3 5.7 - - - +
249A ARG* 2.9 58.8 + - - +
298D ARG* 5.0 7.0 - - - +
299D LYS 3.3 9.6 - - - -
300D PHE* 3.9 26.5 - - - -
24H ILE* 5.6 0.4 - - - -
25H THR* 1.3 73.5 - - - +
27H TYR* 1.3 66.9 + - - +
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Residues in contact with TYR 27 (chain H).
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* 5.6 3.1 - - - -
247A GLU 3.3 7.4 - - - +
248A VAL* 4.0 19.7 - - + -
298D ARG* 3.8 3.1 - - - +
299D LYS* 2.9 34.3 + - + +
301D VAL* 3.4 31.5 - - + +
31E LYS* 5.8 0.2 - - - -
32E SER 4.1 2.6 + - - -
33E THR* 2.8 49.0 + - - +
35E ARG 4.4 2.0 + - - -
36E THR* 4.1 17.7 - - + -
37E PRO* 3.4 32.5 - - + -
39E PHE* 4.0 19.4 - - + -
25H THR* 4.0 19.3 - - + -
26H SER* 1.3 78.2 - - - +
28H ALA* 1.3 63.9 + - - +
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Residues in contact with ALA 28 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A SER* 3.2 7.3 - - - -
247A GLU* 3.0 55.0 + - + +
444A TYR* 5.8 2.9 - - + -
294D GLY* 4.1 17.9 - - - +
298D ARG* 4.3 13.2 - - + +
39E PHE* 4.3 6.1 - - - -
27H TYR* 1.3 77.5 - - - +
29H VAL* 1.3 68.6 + - - +
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Residues in contact with VAL 29 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A GLN* 4.6 1.1 - - - +
244A LEU* 4.4 10.8 - - + -
245A GLY 3.4 9.9 - - - +
246A SER* 4.1 9.6 - - - +
444A TYR* 4.9 6.3 - - - +
294D GLY* 3.8 11.3 + - - -
297D THR* 4.8 3.2 + - - +
39E PHE* 3.8 42.4 - - + -
42E VAL* 6.0 0.9 - - + -
43E LEU* 4.0 22.9 - - + -
28H ALA* 1.3 82.8 - - - +
30H SER* 1.3 78.2 + - - +
31H PRO* 3.7 5.9 - - - +
33H ALA* 4.3 3.6 - - + -
34H GLN* 3.5 23.9 + - + +
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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