Contacts of the strand formed by residues 10 - 14 (chain E) in PDB entry 1KGC
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 TYR 10 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8E PRO* 3.5 15.2 - - - +
9E ARG* 1.3 112.1 + - + +
11E LYS* 1.3 65.0 + - - +
112E THR* 5.0 0.2 - - - -
113E ARG* 3.5 27.8 - - + +
157E HIS* 3.5 40.8 - + + -
158E VAL 4.4 3.7 + - - -
159E GLU* 2.8 30.4 + - + +
218E TYR* 3.5 57.7 - + + +
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Residues in contact with LYS 11 (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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8E PRO* 4.0 18.6 - - + -
10E TYR* 1.3 79.5 - - - +
12E VAL* 1.3 75.7 + - - +
17E GLN* 4.1 12.7 - - - +
18E ASP 5.6 0.2 - - - -
19E VAL* 4.1 26.0 - - + +
21E LEU* 5.1 4.3 - - + -
112E THR* 4.7 5.8 - - + -
113E ARG 3.0 9.8 + - - +
114E LEU* 3.4 24.1 - - + +
115E THR 3.0 24.8 + - - -
157E HIS* 3.5 6.8 + - - -
219E GLY 6.0 0.7 - - - -
221E SER* 4.9 8.7 + - - -
224E ASP* 4.8 10.5 + - - -
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Residues in contact with VAL 12 (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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11E LYS* 1.3 87.5 + - - +
13E ALA* 1.3 63.7 + - - +
17E GLN* 4.7 1.2 - - - +
115E THR* 3.3 12.8 - - + +
117E THR* 4.2 15.3 - - + -
120E LEU* 4.5 8.0 - - + +
123E VAL* 4.0 21.1 - - + -
154E TYR* 5.1 0.9 - - + -
155E PRO* 4.1 26.0 - - + -
157E HIS* 4.8 0.4 - - + -
218E TYR 5.3 0.7 - - - +
219E GLY* 4.0 30.4 + - - +
220E LEU* 4.3 15.5 - - + -
224E ASP* 4.8 9.1 - - - +
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Residues in contact with ALA 13 (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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11E LYS* 4.1 1.3 - - - -
12E VAL* 1.3 76.7 - - - +
14E LYS* 1.3 61.7 + - - +
17E GLN* 3.4 28.5 - - + +
19E VAL* 3.8 19.7 - - + -
82E THR* 4.2 7.2 - - - +
114E LEU* 4.4 9.6 - - + -
115E THR 3.0 7.4 + - - +
116E VAL* 3.3 5.9 - - + -
117E THR* 2.9 27.7 + - - +
120E LEU* 4.3 6.1 - - - -
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Residues in contact with LYS 14 (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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13E ALA* 1.3 73.2 - - - +
15E ARG* 1.3 80.5 + - - +
16E GLY 3.2 0.4 + - - -
17E GLN* 2.9 42.5 + - - +
82E THR* 3.3 3.8 + - - -
117E THR 3.3 5.4 - - - -
118E GLU 3.6 19.5 - - - +
119E ASP* 4.6 7.6 - - - -
120E LEU* 4.1 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