Contacts of the strand formed by residues 195 - 200 (chain A) in PDB entry 3C5H
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 195 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A PHE* 3.3 17.3 - - + +
162A LEU* 4.0 24.9 - - + -
185A TYR* 3.7 27.1 - - + +
188A LEU* 3.6 37.9 - - + -
189A ALA* 3.8 14.4 - - - +
193A LYS 3.4 13.0 + - - +
194A PRO* 1.3 78.9 - - - +
196A VAL* 1.3 71.0 + - - +
223A LEU* 3.2 29.2 - - + +
224A GLN 4.7 1.9 + - - -
246A LEU* 4.1 8.2 - - - +
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Residues in contact with VAL 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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160A PHE 3.0 5.5 + - - -
161A LEU* 3.3 22.0 - - + -
162A LEU 2.8 31.2 + - - -
195A ILE* 1.3 73.8 - - - +
197A VAL* 1.3 71.0 + - - +
198A VAL* 4.0 3.0 - - + +
224A GLN* 3.9 12.1 - - + +
226A VAL* 4.1 20.6 - - + -
239A ALA 4.5 2.0 - - - +
242A THR* 3.9 8.7 - - + -
243A LEU* 3.8 28.0 - - + +
246A LEU* 3.5 30.1 - - + -
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Residues in contact with VAL 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A LEU* 3.4 23.8 - - + +
164A ILE* 3.5 28.9 - - + -
196A VAL* 1.3 77.0 - - - +
198A VAL* 1.3 62.8 + - - +
199A LEU* 3.8 16.2 - - + -
213A ALA 5.3 1.8 - - - +
216A PHE* 4.4 7.2 - - + -
217A ALA* 4.4 5.2 - - + -
223A LEU* 3.6 35.0 - - + +
224A GLN 3.0 13.3 + - - +
225A VAL* 3.3 13.2 - - + -
226A VAL 2.9 25.3 + - - -
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Residues in contact with VAL 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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38A LEU* 3.9 19.5 - - + -
161A LEU* 3.8 40.2 - - + -
162A LEU 2.9 11.4 + - - +
163A GLY* 3.3 6.3 - - - -
164A ILE 2.9 26.3 + - - -
196A VAL* 4.0 3.8 - - + +
197A VAL* 1.3 78.7 - - - +
199A LEU* 1.3 62.3 + - - +
200A THR* 3.6 4.9 + - + +
226A VAL* 3.4 3.6 - - + +
228A THR* 3.4 38.4 - - + +
239A ALA* 3.9 14.4 - - + -
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Residues in contact with LEU 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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164A ILE* 3.4 9.0 - - + +
166A VAL* 4.0 21.3 - - + -
197A VAL* 3.8 20.2 - - + -
198A VAL* 1.3 72.1 - - - +
200A THR* 1.3 58.8 + - - +
202A CYS* 3.8 13.0 - - - -
210A ILE* 3.9 32.3 - - + -
213A ALA* 3.4 26.5 - - + -
214A HIS* 4.1 4.5 - - + +
225A VAL* 3.5 23.6 - - + -
226A VAL 2.9 10.8 + - - +
227A GLU* 4.0 11.2 - - + +
228A THR* 2.7 36.2 + - - +
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Residues in contact with THR 200 (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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33A ILE* 2.6 30.4 + - + +
34A GLY* 4.5 16.4 - - - +
35A LYS* 5.9 0.2 - - - -
38A LEU* 4.6 11.2 - - + -
163A GLY* 4.7 5.6 - - - -
164A ILE 2.8 22.1 + - - +
165A ASP* 3.2 5.2 + - - -
166A VAL* 3.2 25.1 + - - +
198A VAL* 4.1 17.3 - - + +
199A LEU* 1.3 75.8 - - - +
201A LYS* 1.3 73.4 + - - +
202A CYS 3.3 2.7 - - - -
228A THR* 3.7 12.1 - - - +
301A GNP 5.8 0.9 - - - -
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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