Contacts of the strand formed by residues 150 - 155 (chain C) in PDB entry 3DV1
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 PHE 150 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33C THR* 4.0 9.9 - - + -
121C LEU* 3.7 44.6 - - + -
137C PHE* 3.9 29.8 - + + -
149C LEU* 1.3 76.8 - - - +
151C SER* 1.3 58.7 + - - +
152C LEU* 4.2 13.2 - - + -
174C MET* 4.8 5.4 - - + -
175C ILE 3.2 15.3 - - - +
176C ILE* 4.2 7.6 - - + -
178C GLY 4.4 4.0 - - - -
199C TYR* 3.4 21.8 - - - -
344C VAL* 3.9 2.1 - - - +
345C PHE* 2.7 69.5 + + + +
347C ARG* 4.0 8.5 - - - -
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Residues in contact with SER 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 PHE* 1.3 77.8 - - - +
152C LEU* 1.3 64.2 + - - +
173C SER 3.7 0.5 - - - +
174C MET* 3.4 6.2 - - - +
175C ILE* 2.9 35.6 + - - +
178C GLY 3.0 15.8 + - - -
179C ILE* 4.9 0.2 - - - -
342C TYR* 2.6 37.8 + - - -
343C VAL 3.2 11.7 - - - -
344C VAL* 4.0 13.2 - - - -
345C PHE* 4.7 0.2 - - - -
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Residues in contact with LEU 152 (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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6C LEU* 4.2 11.9 - - + -
31C VAL* 4.9 6.3 - - + -
33C THR* 3.7 29.8 - - + -
121C LEU* 5.1 2.0 - - + -
150C PHE* 4.2 6.3 - - + -
151C SER* 1.3 75.0 - - - +
153C GLN* 1.3 60.3 + - - +
154C LEU* 3.8 10.7 + - + +
173C SER 3.4 2.7 - - - +
174C MET* 3.8 40.4 - - + -
229C SER* 3.9 12.6 - - - +
338C MET* 3.9 20.1 - - + +
341C PHE 3.9 2.6 - - - +
342C TYR* 3.7 4.1 - - - -
343C VAL* 2.8 38.8 + - - +
345C PHE* 3.8 13.0 - - + -
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Residues in contact with GLN 153 (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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3C VAL* 5.3 0.5 - - - +
151C SER 4.3 0.2 - - - -
152C LEU* 1.3 72.3 - - - +
154C LEU* 1.3 59.9 + - - +
155C CYS* 3.9 11.4 - - - -
172C GLY* 2.9 8.3 - - - -
173C SER* 2.7 63.7 + - - +
183C LEU* 3.5 35.4 + - + +
341C PHE 4.2 3.6 - - - -
342C TYR* 3.8 19.2 - - + -
357C SER* 3.4 29.4 + - - +
358C ALA* 4.1 4.6 - - - +
359C CYS* 3.9 17.2 - - - +
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Residues in contact with LEU 154 (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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6C LEU* 3.8 28.5 - - + -
14C TYR* 3.7 42.2 - - + +
31C VAL* 5.2 2.5 - - + -
152C LEU* 3.8 21.2 + - + -
153C GLN* 1.3 73.4 - - - +
155C CYS* 1.3 60.9 + - - +
171C GLY 4.3 0.2 - - - -
229C SER* 4.1 24.7 - - - +
335C ALA* 4.8 7.6 - - - -
338C MET* 4.1 25.2 + - + +
339C GLU* 3.2 29.8 - - + +
340C GLY 3.4 6.2 + - - -
341C PHE 4.4 4.5 + - - +
359C CYS* 4.1 2.3 - - - -
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Residues in contact with CYS 155 (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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14C TYR* 2.7 17.6 + - - -
153C GLN* 3.9 18.8 - - - -
154C LEU* 1.3 74.0 - - - +
156C GLY* 1.3 67.0 + - - +
159C PHE* 4.0 15.3 - - + -
170C VAL* 3.6 6.4 - - - +
171C GLY 2.9 26.5 + - - +
172C GLY* 4.3 3.4 - - - -
359C CYS* 2.0 52.7 - - + -
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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