Contacts of the helix formed by residues 53 - 59 (chain B) in PDB entry 5KAL
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 GLY 53 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B PHE* 1.3 83.3 - - - +
54B SER* 1.3 61.8 + - - -
55B THR 3.1 3.1 - - - -
56B VAL* 2.9 18.4 + - - +
57B VAL* 2.9 19.4 + - - +
68B ASP* 3.9 13.9 - - - -
148B SER* 3.5 8.8 + - - -
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Residues in contact with SER 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B GLY* 1.3 72.1 - - - -
55B THR* 1.3 66.8 + - - +
57B VAL* 4.2 10.1 - - - -
58B TYR* 2.9 34.8 + - - +
60B VAL 3.9 3.6 + - - +
61B HIS* 6.1 0.7 - - - -
62B GLU* 4.5 7.1 + - - +
65B SER* 4.5 15.1 - - - -
66B ASP* 4.9 4.5 + - - -
68B ASP* 4.8 2.0 + - - -
169B LYS* 3.7 27.6 + - - -
192B ASN* 6.0 2.9 - - - +
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Residues in contact with THR 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B VAL* 4.4 23.8 - - + -
51B THR* 5.0 12.8 - - + -
52B PHE 4.9 6.5 - - - -
53B GLY 3.1 0.4 - - - -
54B SER* 1.3 80.9 + - - +
56B VAL* 1.3 59.6 + - + +
59B GLY* 2.9 28.7 + - - -
60B VAL 3.6 17.2 + - - +
61B HIS* 3.9 22.1 - - + -
66B ASP 4.4 7.4 + - - -
67B VAL* 4.5 8.5 - - + +
152B ARG* 4.2 0.3 + - - -
221B LEU* 5.9 3.1 - - + -
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Residues in contact with VAL 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B THR* 3.8 16.6 - - + +
52B PHE* 3.6 29.2 - - - +
53B GLY 2.9 8.2 + - - +
55B THR* 1.3 81.7 - - + +
57B VAL* 1.3 65.1 + - - +
58B TYR 3.3 0.4 + - - -
148B SER* 4.5 15.5 - - - +
149B ALA* 5.0 2.9 - - + +
152B ARG* 2.6 55.0 + - + +
222B PRO* 4.0 26.0 - - + -
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Residues in contact with VAL 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B GLY* 2.9 25.2 + - - +
54B SER* 3.3 7.8 + - - +
56B VAL* 1.3 78.0 - - - +
58B TYR* 1.3 71.0 + - + +
148B SER* 4.0 24.9 - - - +
151B LEU* 3.9 22.9 - - + -
152B ARG* 3.8 20.5 - - - +
155B PHE* 3.6 40.8 - - + +
162B ARG* 5.0 0.2 - - - -
192B ASN* 4.2 12.6 - - - +
225B LEU* 5.3 1.4 - - - +
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Residues in contact with TYR 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B SER* 2.9 20.7 + - - +
56B VAL 4.2 0.4 - - - -
57B VAL* 1.3 95.8 - - + +
59B GLY* 1.3 60.6 + - - +
60B VAL* 3.2 21.1 + - + +
62B GLU* 3.3 30.5 - - + -
155B PHE* 4.3 7.0 - + - -
162B ARG* 2.9 51.6 + - + +
165B SER* 2.7 36.0 + - - -
166B MET* 3.7 31.5 + - + -
169B LYS* 4.0 17.9 - - - +
192B ASN* 3.6 8.9 + - - -
225B LEU* 3.8 7.2 - - - +
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Residues in contact with GLY 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B THR* 2.9 21.3 + - - -
56B VAL 3.6 1.6 + - - -
57B VAL 3.5 2.0 - - - -
58B TYR* 1.3 78.6 - - - +
60B VAL* 1.3 57.5 + - - +
152B ARG* 3.8 15.3 - - - -
223B PRO 4.6 3.6 - - - -
224B HIS* 3.2 14.4 - - - -
225B LEU* 2.9 31.1 + - - -
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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