Contacts of the strand formed by residues 191 - 196 (chain C) in PDB entry 4FJV
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 LEU 191 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52C PHE* 3.9 12.8 - - + -
56C LEU* 3.7 17.5 - - + -
180C ILE* 3.6 32.5 - - + +
184C SER* 4.8 3.1 - - - +
189C ILE 4.0 8.1 - - - +
190C ALA* 1.3 74.6 - - - +
192C GLN* 1.3 68.0 + - - +
193C VAL* 3.8 16.8 - - + -
207C VAL* 3.5 4.2 - - - +
208C PHE* 2.8 45.9 + - + +
214C PRO* 4.1 3.3 - - - +
216C VAL* 3.4 32.1 - - + +
218C LEU* 3.8 16.8 - - + -
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Residues in contact with GLN 192 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38C ARG* 3.7 10.1 - - - +
39C PHE* 4.2 0.6 - - - -
191C LEU* 1.3 76.2 - - - +
193C VAL* 1.3 65.8 + - - +
194C GLU* 2.7 28.9 + - + +
205C HIS* 3.3 36.0 + - + -
206C HIS 3.4 4.7 - - - +
207C VAL* 4.0 8.5 - - + +
214C PRO* 3.7 26.7 - - + +
216C VAL 2.8 10.3 + - - -
217C TYR* 3.3 29.5 - - + +
218C LEU 2.9 26.0 + - - +
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Residues in contact with VAL 193 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180C ILE* 5.1 4.3 - - + -
191C LEU* 3.8 27.8 - - + -
192C GLN* 1.3 77.0 - - - +
194C GLU* 1.3 63.5 + - - +
195C TYR* 3.6 1.4 + - - +
205C HIS* 3.1 7.7 - - - -
206C HIS* 2.9 43.9 + - + +
208C PHE* 4.1 13.5 - - + -
218C LEU* 3.6 8.5 - - + +
220C TYR* 3.6 30.1 - - + -
225C TYR* 4.0 19.7 - - + -
73D LEU* 4.6 12.8 - - + -
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Residues in contact with GLU 194 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C LEU* 3.6 14.8 - - + +
38C ARG* 2.9 34.1 + - - -
39C PHE* 3.8 19.7 - - + -
192C GLN* 2.7 30.8 + - + +
193C VAL* 1.3 70.2 - - - +
195C TYR* 1.3 60.4 + - - +
196C VAL* 3.7 1.4 + - + +
203C LEU* 4.4 7.1 - - - +
204C ASN 4.1 5.9 - - - +
205C HIS* 3.5 13.5 + - - +
217C TYR* 5.7 0.4 - - + -
218C LEU 2.9 15.2 + - - +
219C LEU* 3.8 6.9 - - + +
220C TYR* 2.8 32.9 + - - +
228C LEU* 3.8 15.5 - - + -
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Residues in contact with TYR 195 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C LYS* 5.3 1.4 + - - -
193C VAL* 3.6 3.7 + - + +
194C GLU* 1.3 72.2 + - - +
196C VAL* 1.3 65.5 + - - +
197C ASP* 3.3 35.5 + - + +
203C LEU* 3.9 13.0 - - - +
204C ASN* 2.9 38.4 + - - +
206C HIS* 4.3 5.2 - + + +
220C TYR* 3.5 36.8 + + - -
39D ASP* 5.1 3.5 + - - +
40D GLN* 3.4 47.3 - - + +
72D ARG* 3.6 18.8 + - - +
73D LEU* 4.1 12.1 - - + -
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Residues in contact with VAL 196 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C TYR* 3.9 22.1 + - + +
31C LYS* 3.8 26.9 - - + -
32C ILE* 5.6 4.0 - - + -
35C LEU* 4.3 14.8 - - + -
194C GLU* 4.5 1.8 - - + +
195C TYR* 1.3 84.7 - - - +
197C ASP* 1.3 60.5 + - - +
203C LEU* 3.9 14.4 - - + -
219C LEU* 3.5 26.7 - - + -
220C TYR 3.0 20.9 + - - +
221C LYS* 3.7 26.6 - - + +
222C THR 4.4 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