Contacts of the strand formed by residues 146 - 151 (chain C) in PDB entry 3V56
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 CYS 146 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B TYR* 4.1 15.7 - - - -
250B ILE* 4.0 10.3 - - + -
284B LEU* 4.3 13.9 - - - -
144C GLN 4.0 3.1 - - - -
145C ASP* 1.3 75.5 - - - +
147C LEU* 1.3 60.1 + - - +
172C PHE* 4.1 10.6 - - - +
173C LYS* 3.6 1.0 - - - +
174C ARG* 2.8 61.6 + - - +
178C LEU* 4.1 5.8 - - - +
281C ALA 3.3 14.8 - - - +
282C LEU* 4.0 11.9 - - + -
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Residues in contact with LEU 147 (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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146C CYS* 1.3 75.6 - - - +
148C GLN* 1.3 62.6 + - - +
149C LEU* 3.8 24.2 - - + -
170C LEU* 3.9 20.4 - - + -
172C PHE* 3.6 6.5 - - - +
173C LYS* 3.9 10.5 - - + -
178C LEU* 3.8 22.1 - - + +
179C GLU* 3.6 38.8 - - - +
180C GLU* 3.7 4.0 - - - +
185C ILE* 3.8 29.4 - - + -
196C TYR* 4.2 1.4 + - - -
280C GLY* 3.2 3.1 - - - -
281C ALA 3.0 31.2 + - - +
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Residues in contact with GLN 148 (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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230B PHE* 4.4 12.2 - - - -
249B GLY* 4.0 2.1 - - - -
250B ILE 3.0 35.3 + - - +
147C LEU* 1.3 73.3 - - - +
149C LEU* 1.3 74.4 + - - +
150C ILE* 4.2 9.7 - - - +
170C LEU* 3.8 5.2 - - - +
171C SER* 3.0 33.2 + - - -
172C PHE* 3.0 38.4 + - + +
196C TYR* 2.7 33.4 + - + +
278C PHE* 4.9 4.7 - - + +
279C PHE 3.6 6.7 - - - +
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Residues in contact with LEU 149 (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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147C LEU* 3.8 17.0 - - + -
148C GLN* 1.3 74.4 - - - +
150C ILE* 1.3 63.1 + - - +
168C TRP* 3.8 41.7 - - + -
169C LEU 3.4 12.8 - - - +
170C LEU* 4.0 11.9 - - + -
180C GLU* 3.8 26.7 - - + -
183C ASN 5.1 0.9 - - - +
184C LYS 4.9 8.7 - - - -
185C ILE* 3.7 25.6 - - + -
278C PHE* 3.3 7.1 - - - +
279C PHE* 2.7 47.4 + - + +
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Residues in contact with ILE 150 (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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148C GLN* 4.2 10.5 - - - +
149C LEU* 1.3 77.9 - - - +
151C ALA* 1.3 65.7 + - - +
168C TRP* 3.5 5.2 - - - -
169C LEU* 2.9 53.3 + - + +
170C LEU 5.6 0.2 - - - -
171C SER* 3.9 31.2 - - - +
274C GLY* 3.4 33.4 - - - +
277C THR 3.8 3.8 - - - -
278C PHE* 4.0 7.0 - - + -
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Residues in contact with ALA 151 (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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150C ILE* 1.3 77.0 - - - +
152C ASP* 1.3 60.0 + - - +
153C SER* 3.4 5.4 + - - -
166C VAL* 3.9 7.4 - - + -
167C PRO 3.7 6.1 - - - -
168C TRP* 3.6 5.8 - - - -
169C LEU* 4.6 3.2 - - - +
272C LEU* 3.4 35.3 - - + +
273C ASP 4.3 1.3 - - - +
274C GLY* 4.1 9.1 + - - -
277C THR* 3.0 36.4 + - + +
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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