Contacts of the helix formed by residues 134 - 142 (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 SER 134 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126D TYR* 3.7 24.1 - - - +
127D GLN 3.5 26.2 + - - -
128D LEU* 4.4 6.0 - - - +
129D ARG* 5.5 0.9 - - - +
132E GLU 3.8 0.8 + - - -
133E PRO* 1.3 72.2 - - - +
135E GLU* 1.3 63.8 + - - +
136E ALA* 3.1 21.3 + - - +
137E GLU* 3.2 24.5 + - - +
138E ILE* 3.2 17.1 + - - +
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Residues in contact with GLU 135 (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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129D ARG* 4.7 19.9 + - - +
133E PRO 3.6 6.2 + - - +
134E SER* 1.3 72.3 + - - +
136E ALA* 1.3 56.6 + - - +
138E ILE* 3.4 29.1 + - - +
139E SER* 3.1 28.2 + - - -
204E TRP* 5.6 0.7 + - - -
205E GLN* 5.3 2.6 + - - -
246E ALA 5.3 0.9 - - - +
247E ASP* 3.6 34.7 - - - +
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Residues in contact with ALA 136 (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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126D TYR* 3.9 2.0 - - - -
203D PHE* 4.9 2.7 - - + -
205D PRO* 3.5 39.3 - - + -
134E SER* 3.1 10.0 + - - +
135E GLU* 1.3 77.3 - - - +
137E GLU* 1.3 66.5 + - - +
139E SER* 3.4 5.4 + - - -
140E HIS* 2.9 26.7 + - - +
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Residues in contact with GLU 137 (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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126D TYR* 3.5 41.3 - - + -
128D LEU* 6.1 0.3 - - - +
140D LEU* 4.5 5.6 - - - +
133E PRO* 4.6 0.2 - - - +
134E SER* 3.2 19.0 + - - +
136E ALA* 1.3 77.6 - - - +
138E ILE* 1.3 55.4 + - - +
141E THR* 2.7 47.1 + - - +
143E LYS 3.3 12.1 - - - +
144E ALA* 3.7 1.9 - - - -
145E THR* 2.7 51.2 + - - +
198E ARG* 2.9 23.8 + - - +
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Residues in contact with ILE 138 (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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133E PRO* 4.3 8.1 - - + +
134E SER 3.2 13.9 + - - +
135E GLU* 3.5 31.9 - - - +
136E ALA 3.3 0.2 - - - -
137E GLU* 1.3 77.7 - - - +
139E SER* 1.3 58.4 + - - +
142E GLN* 2.9 30.4 + - - +
143E LYS 3.4 17.3 - - - +
144E ALA* 4.1 9.9 - - + -
201E ALA* 3.8 19.5 - - + -
204E TRP* 3.6 33.2 - - + +
205E GLN* 3.8 18.6 - - + +
247E ASP* 6.0 0.2 - - - +
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Residues in contact with SER 139 (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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135E GLU 3.1 17.5 + - - -
136E ALA* 3.9 5.8 - - - -
137E GLU 3.3 0.2 - - - -
138E ILE* 1.3 77.6 - - - +
140E HIS* 1.3 58.3 - - - +
142E GLN* 2.9 20.6 + - - +
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Residues in contact with HIS 140 (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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122D ASP* 2.8 44.3 + - - +
124D ALA* 5.0 1.3 - - + -
126D TYR* 3.3 24.0 - - - +
203D PHE* 3.9 38.0 - + + +
136E ALA 2.9 17.9 + - - +
139E SER* 1.3 80.7 - - - +
141E THR* 1.3 57.7 + - + +
142E GLN* 4.4 2.6 + - - +
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Residues in contact with THR 141 (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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122D ASP* 3.7 19.1 - - - +
126D TYR* 3.6 22.2 - - - +
143D ASP* 3.8 15.5 - - - +
137E GLU* 2.7 30.7 + - + +
140E HIS* 1.3 76.6 - - - +
142E GLN* 1.3 72.8 + - - +
143E LYS* 3.0 39.6 + - - +
198E ARG* 3.8 4.9 + - - +
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Residues in contact with GLN 142 (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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138E ILE* 2.9 20.2 + - - +
139E SER* 2.9 28.9 + - - +
140E HIS 4.4 2.8 + - - +
141E THR* 1.3 82.1 - - - +
143E LYS* 1.3 61.8 + - - +
200E SER* 3.8 5.5 - - - -
201E ALA* 2.9 32.6 + - + +
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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