Contacts of the helix formed by residues 261 - 269 (chain B) in PDB entry 3N9Y
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 GLY 261 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B LEU* 5.0 0.9 - - - +
174B VAL 3.4 12.6 - - - -
175B ILE 3.8 4.5 - - - -
177B GLY* 4.3 5.6 - - - -
259B TYR* 3.4 24.3 - - - -
260B ARG* 1.3 80.3 - - - +
262B ILE* 1.3 66.0 + - - -
263B LEU 3.4 2.2 - - - -
264B TYR* 3.5 3.6 + - - +
265B ARG* 3.4 23.4 + - - +
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Residues in contact with ILE 262 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B GLU* 4.0 13.2 - - + +
119B VAL* 3.6 32.1 - - + -
128B PHE* 3.7 30.1 - - + -
174B VAL* 2.9 25.1 + - + +
175B ILE* 3.3 15.0 + - + -
259B TYR* 3.4 4.0 + - - +
261B GLY* 1.3 70.4 - - - -
263B LEU* 1.3 63.8 + - - +
265B ARG* 3.1 9.3 + - - +
266B LEU* 3.0 38.7 + - + +
281B VAL* 6.3 1.1 - - + -
284B MET* 3.8 19.5 - - + -
428B ILE* 4.1 7.0 - - + -
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Residues in contact with LEU 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175B ILE* 3.0 24.5 + - + +
176B PHE* 3.7 25.8 - - + -
242B THR* 4.0 20.4 - - + +
245B PHE* 3.5 35.2 - - + -
262B ILE* 1.3 77.7 - - - +
264B TYR* 1.3 58.0 + - - +
266B LEU* 3.2 3.8 + - + +
267B LEU* 2.9 41.5 + - + +
277B ILE* 3.5 31.6 - - + -
281B VAL* 3.9 13.0 - - + -
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Residues in contact with TYR 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245B PHE* 3.8 16.9 - + + -
249B LEU* 3.5 35.9 - - + +
254B SER 3.4 10.8 + - - -
255B VAL* 3.9 4.7 - - - +
256B HIS* 3.2 51.9 + + + -
258B ASP 5.7 0.7 - - - -
260B ARG* 3.6 33.9 - - + +
261B GLY 3.5 11.1 + - - +
263B LEU* 1.3 77.6 - - - +
265B ARG* 1.3 66.4 + - + +
267B LEU* 3.6 3.1 + - - +
268B GLY* 2.9 30.3 + - - -
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Residues in contact with ARG 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLN 5.4 0.2 + - - -
118B GLU* 3.0 48.6 + - - +
123B GLU 5.3 1.0 + - - -
124B ALA* 4.5 11.7 - - - +
126B LYS* 5.9 0.2 - - - +
127B ASN* 3.5 14.5 - - - +
259B TYR* 3.5 36.4 - - + +
260B ARG 6.1 0.2 - - - +
261B GLY 3.4 14.1 + - - +
262B ILE* 3.1 9.9 + - - +
264B TYR* 1.3 88.1 - - + +
266B LEU* 1.3 56.6 + - - +
269B ASP* 3.0 43.9 + - - +
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Residues in contact with LEU 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ALA 4.2 13.7 - - - +
115B LEU* 4.0 24.9 - - + -
118B GLU* 3.7 24.5 - - + -
262B ILE* 3.0 33.6 + - + +
263B LEU* 3.9 6.1 - - + +
265B ARG* 1.3 76.4 - - - +
267B LEU* 1.3 62.4 + - - +
268B GLY 3.4 0.3 + - - -
270B SER* 3.1 43.9 + - - +
272B MET* 4.9 4.4 - - - +
277B ILE* 3.4 38.1 - - + +
280B ASN* 6.2 0.2 - - + -
281B VAL* 5.3 6.1 - - + -
284B MET* 5.9 1.3 - - - -
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242B THR 5.3 0.7 - - - +
245B PHE* 4.0 16.2 - - + -
246B TYR* 4.0 25.6 - - + +
249B LEU* 4.2 20.8 - - + +
250B ARG* 5.8 4.2 + - - +
263B LEU* 2.9 43.5 + - + +
264B TYR 4.2 2.0 - - - +
266B LEU* 1.3 76.0 - - - +
268B GLY* 1.3 61.8 - - - +
274B PHE* 3.7 32.5 - - + -
277B ILE* 4.2 17.3 - - + -
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Residues in contact with GLY 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249B LEU* 6.1 1.1 - - - -
264B TYR* 2.9 22.4 + - - -
265B ARG* 3.3 1.3 + - - -
266B LEU 3.2 0.2 - - - -
267B LEU* 1.3 80.9 - - - +
269B ASP* 1.3 65.6 + - - +
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Residues in contact with ASP 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B GLU* 5.0 9.2 - - - +
265B ARG* 3.0 26.6 + - - +
266B LEU* 5.8 0.2 - - - +
268B GLY* 1.3 81.4 - - - +
270B SER* 1.3 61.3 + - - +
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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