Contacts of the strand formed by residues 191 - 195 (chain A) in PDB entry 1E1K
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 THR 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ASP 3.2 2.7 + - - -
147A THR* 3.3 19.0 + - + +
148A ALA 2.8 25.3 + - - -
189A VAL* 3.7 2.0 - - - +
190A LYS* 1.3 85.9 + - - +
192A VAL* 1.3 68.8 + - - +
193A TRP* 3.5 35.9 - - + +
222A MET* 4.1 15.3 - - + -
271A ALA* 3.2 7.9 + - - +
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Residues in contact with VAL 192 (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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148A ALA* 3.4 14.6 - - + +
150A ILE* 3.6 31.4 - - + -
161A ALA* 3.7 13.9 - - + +
164A LEU* 4.2 11.4 - - + -
165A LEU* 3.7 34.3 - - + -
189A VAL* 4.1 11.0 - - + -
191A THR* 1.3 80.9 - - - +
193A TRP* 1.3 68.3 + - - +
194A ILE* 4.3 2.4 - - + +
271A ALA 3.0 8.7 + - - -
272A TRP* 3.1 7.0 - - + +
273A GLY 2.9 25.5 + - - +
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Residues in contact with TRP 193 (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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147A THR* 3.8 23.4 - - + +
148A ALA 3.0 8.8 + - - +
149A VAL* 3.6 3.0 - - + -
150A ILE* 2.8 27.9 + - - +
191A THR* 3.5 18.5 - - + +
192A VAL* 1.3 76.1 - - - +
194A ILE* 1.3 62.8 + - - +
195A VAL* 3.9 15.4 - - + +
222A MET* 3.4 43.3 - - + -
273A GLY* 3.5 22.9 - - - -
275A ARG* 3.6 33.2 - - + -
320A LEU* 4.1 32.3 - - + +
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Residues in contact with ILE 194 (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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150A ILE* 3.5 9.4 - - + +
152A GLY 3.4 24.2 - - - +
153A GLN* 3.0 22.7 + - + -
157A ALA* 4.0 14.8 - - + +
158A LEU* 3.5 31.6 - - + -
161A ALA* 3.8 26.2 - - + -
192A VAL* 4.3 7.2 - - + +
193A TRP* 1.3 75.5 - - - +
195A VAL* 1.3 58.0 + - - +
205A PHE* 5.8 0.2 - - + -
213A MET* 5.4 0.4 - - + -
272A TRP* 4.5 10.3 - - + -
273A GLY 2.8 15.6 + - - +
274A LEU* 3.4 15.8 - - + -
275A ARG 2.9 22.2 + - - -
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Residues in contact with VAL 195 (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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149A VAL* 3.9 18.4 - - + -
150A ILE 3.0 15.7 + - - +
151A LEU* 3.6 11.6 - - + +
152A GLY 2.9 26.7 + - - -
153A GLN* 3.9 2.9 - - - -
193A TRP* 4.1 11.9 - - + +
194A ILE* 1.3 75.1 - - - +
196A GLY* 1.3 61.3 + - - +
275A ARG* 3.4 21.5 - - + +
278A ARG* 3.6 36.2 - - + +
297A LEU* 4.3 16.8 - - + -
320A LEU* 4.7 6.7 - - + -
802A NAP 5.3 2.3 + - - -
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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