Contacts of the strand formed by residues 193 - 199 (chain A) in PDB entry 1CEC
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 ILE 193 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A ILE* 4.4 2.2 - - + -
168A TRP* 3.6 5.9 - - - -
169A LEU* 3.3 18.4 - - + +
171A ILE* 3.4 35.9 - - + -
188A ILE* 4.2 16.4 - - + -
190A ASP* 3.5 38.8 + - + +
191A ASP 3.5 4.0 + - - +
192A TYR* 1.3 86.4 - - - +
194A VAL* 1.3 76.0 + - - +
195A TYR* 3.9 34.7 - - + +
274A CYS* 5.5 0.9 - - - +
275A LYS* 4.5 9.9 + - - +
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Residues in contact with VAL 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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168A TRP* 3.4 30.3 - - + -
169A LEU 2.9 5.7 + - - -
170A TYR* 3.2 35.3 - - + +
171A ILE 2.9 25.3 + - - -
193A ILE* 1.3 76.1 - - - +
195A TYR* 1.3 64.3 + - - +
275A LYS* 3.8 27.1 - - + +
276A LEU 4.1 4.5 - - - +
277A TYR* 3.6 30.1 - - + -
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Residues in contact with TYR 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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171A ILE* 3.3 10.5 - - + +
182A LEU* 4.0 11.0 - - + -
185A LEU* 3.7 33.0 - - + -
186A ALA 5.0 1.4 + - - -
188A ILE* 3.7 32.6 + - + +
193A ILE* 3.9 21.1 - - + +
194A VAL* 1.3 75.4 - - - +
196A ASN* 1.3 56.3 + - - +
197A PHE* 4.7 0.2 - - - -
268A PHE* 3.7 24.0 - + + -
272A LYS* 3.8 25.3 + - + -
274A CYS* 3.7 36.1 - - + -
275A LYS 2.9 11.2 + - - +
276A LEU* 3.3 12.3 - - + +
277A TYR 2.7 31.7 + - - +
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Residues in contact with ASN 196 (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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136A GLU* 3.2 24.2 + - + +
170A TYR* 4.9 4.3 - - + -
171A ILE 2.9 21.6 + - - +
172A GLY* 3.5 15.7 - - - +
173A GLY 4.3 0.3 + - - -
177A ASN* 2.9 31.7 + - - +
182A LEU* 3.7 11.0 - - - +
194A VAL 3.9 0.2 + - - -
195A TYR* 1.3 74.8 - - - +
197A PHE* 1.3 64.8 + - - +
198A HIS* 3.2 11.1 + - - -
277A TYR* 3.1 16.2 - - + -
279A GLY* 2.9 34.1 + - - -
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Residues in contact with PHE 197 (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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177A ASN* 3.1 14.8 - - - +
178A SER 4.3 0.9 - - - +
179A PRO* 3.8 30.1 - - + -
182A LEU* 4.5 8.5 - - + -
195A TYR 4.7 1.1 - - - -
196A ASN* 1.3 78.0 - - - +
198A HIS* 1.3 75.3 + - - +
199A PHE* 4.3 3.8 - + + -
262A LEU* 3.5 27.8 - - + -
265A ALA* 4.1 16.6 - - + -
276A LEU* 4.4 7.9 - - + -
277A TYR 3.0 26.2 + - - -
278A CYS* 3.2 38.2 - - + -
279A GLY 3.2 5.5 + - - -
299A TYR* 3.4 21.5 - - - -
303A LEU* 4.6 0.7 - - + -
308A ILE* 4.1 18.2 - - + -
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Residues in contact with HIS 198 (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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46A ARG* 3.2 24.0 + - - -
139A ASN* 4.0 11.0 - - + -
176A TYR* 3.4 23.3 + - - +
177A ASN* 2.8 26.7 + - + +
178A SER* 5.0 0.3 - - - -
179A PRO* 3.5 22.0 - - - +
196A ASN* 3.2 20.0 + - - -
197A PHE* 1.3 83.0 - - - +
199A PHE* 1.3 63.1 + - - +
200A TYR* 4.3 11.4 - - + -
201A ASN* 5.3 0.2 - - - +
279A GLY 4.1 1.1 - - - -
280A GLU* 3.3 44.5 + - + +
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Residues in contact with PHE 199 (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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179A PRO* 4.9 3.6 - - + -
197A PHE* 4.3 5.8 - + + -
198A HIS* 1.3 77.3 - - - +
200A TYR* 1.3 62.1 + - - +
201A ASN* 3.6 39.0 - - + -
258A LEU* 3.7 28.0 - - + -
261A ASP* 3.7 24.7 - - + -
262A LEU* 3.9 20.2 - - + -
278A CYS* 3.9 4.9 - - - -
280A GLU 2.8 9.3 + - - -
281A PHE* 3.1 24.6 - - - +
295A TRP* 3.8 14.4 - + - -
299A TYR* 3.1 53.6 - + + +
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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