Contacts of the strand formed by residues 255 - 260 (chain C) in PDB entry 1I9R
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 SER 255 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A LEU* 4.6 9.5 - - - +
226A GLY 5.3 0.5 + - - -
125C HIS* 3.1 36.9 + - - -
126C VAL 3.5 9.2 - - - -
127C ILE* 5.3 1.8 - - - -
140C TRP* 3.2 7.3 - - - -
172C TYR* 5.2 0.8 - - - -
173C ALA* 3.5 1.7 - - - -
174C GLN* 2.8 46.6 + - - +
252C GLY 4.9 3.6 + - - -
253C PHE 4.5 2.8 + - - -
254C THR* 1.3 75.1 - - - +
256C PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 256 (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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125C HIS* 3.7 1.3 + - - -
126C VAL* 2.9 36.9 + - + +
140C TRP* 3.3 52.3 - + + -
159C LYS 4.4 0.9 - - - -
160C GLN* 4.6 0.4 - - - -
161C LEU* 3.4 36.6 - - + -
171C ILE* 4.6 5.4 - - + -
172C TYR* 3.2 28.0 - - - -
173C ALA* 4.0 0.9 - - - +
193C LEU* 4.3 11.2 - - + -
237C VAL* 3.7 38.6 - - + -
238C PHE* 4.0 7.0 - - - -
239C VAL* 3.6 20.0 - - + -
255C SER* 1.3 77.5 - - - +
257C GLY* 1.3 60.8 + - - +
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Residues in contact with GLY 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124C ALA 2.7 17.3 - - - -
161C LEU* 3.9 11.0 - - - -
171C ILE* 3.7 2.0 - - - +
172C TYR* 2.9 55.4 + - - +
256C PHE* 1.3 74.5 - - - +
258C LEU* 1.3 62.6 + - - +
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Residues in contact with LEU 258 (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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228A VAL* 5.3 0.4 - - - -
122C ILE* 4.6 3.1 - - + -
123C ALA* 2.9 1.6 - - - -
124C ALA* 2.8 38.9 + - + +
153C VAL* 3.5 26.7 - - + -
161C LEU* 3.9 33.7 - - + +
163C VAL* 4.2 12.8 - - + -
169C TYR* 4.0 20.4 - - + -
170C TYR 3.2 11.7 - - - +
171C ILE* 3.8 18.2 - - + -
172C TYR* 3.8 3.7 - - - -
231C LEU* 5.3 2.5 - - + -
237C VAL* 4.1 15.0 - - + -
257C GLY* 1.3 73.4 - - - +
259C LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 259 (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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170A TYR* 4.1 15.0 - - + -
228A VAL* 3.4 33.2 - - + -
259A LEU* 6.3 0.9 - - + -
261A LEU* 4.1 21.1 - - + -
259B LEU* 6.4 0.4 - - + -
122C ILE 3.4 4.3 - - - -
123C ALA* 3.9 9.0 - - + -
169C TYR* 3.3 5.0 - - - -
170C TYR* 2.7 64.2 + - + +
172C TYR* 4.7 2.2 - - + -
258C LEU* 1.3 78.2 - - - +
260C LYS* 1.3 65.1 + - - +
261C LEU* 3.5 19.5 - - + +
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Residues in contact with LYS 260 (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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261A LEU* 5.5 5.2 - - - +
121B GLN* 5.3 2.4 - - - +
121C GLN* 5.7 1.4 - - - +
122C ILE* 2.9 44.6 + - + +
165C ARG* 4.5 10.8 - - + +
166C GLN 3.7 24.0 - - - -
167C GLY* 4.5 4.7 - - - -
168C LEU 3.7 9.4 - - - +
169C TYR* 3.2 39.9 - - + +
259C LEU* 1.3 75.7 - - - +
261C LEU* 1.3 80.8 + - - +
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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