Contacts of the strand formed by residues 102 - 108 (chain E) in PDB entry 1KYZ
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 VAL 102 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302A VAL* 3.9 34.8 - - + -
334A GLU* 5.7 4.7 - - - +
94E VAL* 4.2 9.0 - - + -
95E ARG 3.5 4.3 - - - -
96E THR* 4.1 15.9 - - + +
100E GLY 5.5 1.3 - - - +
101E LYS* 1.3 79.1 - - - +
103E GLN* 1.3 59.6 + - - +
104E ARG* 4.1 19.6 + - - +
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Residues in contact with GLN 103 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E SER* 3.6 23.3 + - - -
59E PRO* 4.7 3.7 - - + +
60E ILE* 3.9 20.6 - - - +
93E SER 3.9 0.5 - - - +
94E VAL* 3.6 1.5 - - - -
95E ARG* 2.6 85.5 + - + +
97E GLN* 3.4 18.6 + - + +
101E LYS 4.7 3.4 - - - +
102E VAL* 1.3 75.6 - - - +
104E ARG* 1.3 77.5 + - - +
105E LEU* 3.9 2.0 - - + +
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Residues in contact with ARG 104 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A VAL* 3.3 26.4 + - - +
304A PRO* 4.4 6.3 - - - -
58E SER* 3.6 2.9 - - - -
59E PRO* 3.1 29.1 - - - +
78E ASP* 2.6 38.2 + - - +
82E ARG* 3.9 26.5 - - - +
92E CYS* 3.8 17.9 - - - -
93E SER 3.7 3.4 - - - -
94E VAL* 4.0 13.9 - - + -
102E VAL* 4.1 28.4 + - - +
103E GLN* 1.3 76.9 - - - +
105E LEU* 1.3 63.6 + - - +
106E TYR* 3.4 27.9 + - + -
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Residues in contact with LEU 105 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E GLN* 3.9 27.4 + - + +
57E ILE* 3.5 3.6 - - - -
58E SER* 3.6 31.4 - - - +
61E GLU* 4.9 1.8 - - - +
92E CYS* 3.2 7.8 - - - -
93E SER* 3.0 49.1 + - - +
95E ARG* 3.5 49.4 - - + +
103E GLN* 3.9 3.6 - - + +
104E ARG* 1.3 74.8 - - - +
106E TYR* 1.3 62.3 + - - +
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Residues in contact with TYR 106 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304A PRO* 5.1 0.4 - - + -
48E ILE* 4.0 22.3 - - + +
56E GLN* 3.1 5.1 - - - -
57E ILE* 2.7 46.5 + - - +
59E PRO* 3.9 14.4 - - + -
62E ILE* 4.8 1.1 - - + -
78E ASP* 2.6 37.1 + - - -
81E LEU* 3.5 47.3 - - + -
82E ARG* 3.3 11.3 + - - +
85E ALA* 4.0 6.1 - - + -
90E LEU* 4.2 9.0 - - + -
91E THR 3.4 12.6 - - - +
92E CYS* 3.9 14.8 - - + -
104E ARG* 3.4 30.8 - - + -
105E LEU* 1.3 75.9 - - - +
107E GLY* 1.3 57.8 + - - +
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Residues in contact with GLY 107 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E ILE* 3.8 9.4 - - - -
55E ALA 3.3 19.3 - - - -
56E GLN* 4.0 2.1 - - - +
90E LEU* 3.2 11.5 - - - +
91E THR* 2.7 45.4 + - - -
106E TYR* 1.3 74.5 - - - +
108E LEU* 1.3 55.4 + - - -
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Residues in contact with LEU 108 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45E LEU* 3.9 20.2 - - + +
48E ILE* 3.7 13.1 - - + +
49E ALA* 3.6 39.3 - - + +
54E GLY* 6.1 1.4 - - - -
55E ALA 4.4 2.2 + - - -
89E ILE 4.3 1.1 - - - -
90E LEU* 3.8 20.4 - - + -
91E THR* 4.2 7.2 + - - +
107E GLY* 1.3 72.9 - - - -
109E ALA* 1.3 67.3 + - - +
110E THR* 3.9 1.6 + - - +
112E ALA* 4.6 11.2 - - + -
116E VAL* 3.7 26.2 - - + -
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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