Contacts of the strand formed by residues 32 - 37 (chain A) in PDB entry 5TK5
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 LEU 32 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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28A HIS* 3.3 23.4 - - - +
30A GLU 3.8 5.4 + - - -
31A GLN* 1.3 82.3 - - - +
33A LYS* 1.3 63.4 + - - +
34A VAL* 3.5 7.8 + - + -
104A VAL* 3.7 26.9 - - + -
105A GLU 3.8 6.5 - - - +
227A ASP* 3.1 28.0 + - + +
228A VAL 4.4 0.9 - - - -
229A TRP* 3.8 26.7 - - + +
255A LEU* 4.5 3.6 - - + -
275A VAL* 3.5 25.4 - - + +
276A THR 4.7 0.4 - - - -
277A GLN* 3.8 33.0 - - + +
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Residues in contact with LYS 33 (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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26A LEU* 4.0 15.0 - - + -
28A HIS 3.4 3.6 - - - -
29A GLN* 2.9 33.3 + - + +
30A GLU* 3.0 20.3 + - - +
32A LEU* 1.3 68.7 - - - +
34A VAL* 1.3 61.6 + - - +
35A MET* 3.8 5.7 + - + +
103A VAL 3.6 2.6 - - - +
104A VAL* 3.3 7.0 - - - +
105A GLU* 2.8 53.1 + - + +
106A ARG 4.0 11.2 - - - +
107A ARG* 3.8 27.3 - - - +
108A ARG* 5.5 0.9 - - - +
135A LYS 4.4 16.5 + - - -
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Residues in contact with VAL 34 (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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26A LEU* 3.5 2.3 - - - -
27A MET* 2.7 38.2 + - + +
28A HIS* 2.9 37.5 + - + -
32A LEU* 4.2 20.4 - - + +
33A LYS* 1.3 73.4 - - - +
35A MET* 1.3 54.3 + - - +
36A PHE* 4.1 11.4 - - + -
102A LEU* 3.8 22.9 - - + -
103A VAL 4.0 1.8 - - - -
104A VAL* 4.6 6.7 - - + -
229A TRP* 4.0 36.8 - - + -
255A LEU* 4.9 0.7 - - + -
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Residues in contact with MET 35 (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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24A ASN* 4.9 10.5 - - - +
25A LYS 3.7 8.3 - - - +
26A LEU* 3.9 18.2 - - + -
33A LYS* 4.2 14.8 - - + -
34A VAL* 1.3 75.0 - - - +
36A PHE* 1.3 66.8 + - - +
37A ILE* 3.8 24.2 - - + -
101A GLY 3.7 0.3 - - - +
102A LEU* 3.4 5.7 - - - +
103A VAL* 2.9 56.3 + - + +
105A GLU* 3.7 37.9 - - + +
137A LEU* 6.0 4.7 - - + -
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Residues in contact with PHE 36 (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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7A VAL* 3.7 26.7 - - + -
10A TRP* 3.4 22.2 - + + -
11A VAL* 3.8 14.4 - - + -
18A PHE* 3.4 24.7 - - + -
24A ASN* 3.2 5.4 - - - +
25A LYS 3.0 30.9 + - - -
27A MET* 3.8 33.7 - - + -
34A VAL* 4.1 10.3 - - + -
35A MET* 1.3 74.7 - - - +
37A ILE* 1.4 61.0 + - - +
58A LEU* 3.6 32.3 - - + -
100A VAL* 4.0 8.3 - - + -
101A GLY 3.2 6.1 - - - +
102A LEU* 3.9 16.6 - - + -
229A TRP* 4.6 7.2 - + - -
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Residues in contact with ILE 37 (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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18A PHE* 4.5 2.7 - - - -
23A CYS* 3.3 14.8 - - + +
24A ASN* 3.9 12.6 - - + -
35A MET* 3.8 28.5 - - + -
36A PHE* 1.4 80.3 - - - +
38A GLY* 1.3 71.5 + - - +
41A ASN* 6.0 2.7 - - + +
93A PRO* 6.5 0.9 - - + -
95A ARG* 3.6 29.4 + - - +
99A THR* 4.4 0.5 + - - -
100A VAL* 3.5 3.4 - - - +
101A GLY* 2.8 37.9 + - - +
103A VAL* 3.7 26.9 - - + -
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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