Contacts of the helix formed by residues 257 - 268 (chain A) in PDB entry 2QNJ
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 ASN 257 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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255A GLY 3.3 3.2 - - - -
256A GLN* 1.3 85.7 - - - +
258A LEU* 1.3 64.3 + - - +
259A LYS* 3.5 9.6 + - - +
260A GLU* 3.0 28.3 + - - +
261A LEU* 3.1 20.1 + - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO* 4.5 26.2 - - + -
224A PHE* 5.4 13.0 - - + -
257A ASN* 1.3 72.5 - - - +
259A LYS* 1.3 65.0 + - - +
261A LEU* 3.1 12.6 + - + +
262A ARG* 2.8 23.8 + - - +
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Residues in contact with LYS 259 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257A ASN* 3.4 8.4 + - - +
258A LEU* 1.3 75.2 - - - +
260A GLU* 1.3 58.5 + - - +
262A ARG* 3.0 19.4 + - - +
263A GLU* 2.8 34.3 + - - +
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Residues in contact with GLU 260 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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254A ASP 4.3 2.5 - - - -
255A GLY* 3.2 9.7 - - - -
256A GLN* 2.9 37.2 + - - +
257A ASN* 3.0 24.9 + - - +
259A LYS* 1.3 74.6 - - - +
261A LEU* 1.3 66.8 + - - +
263A GLU* 3.4 11.1 + - + +
264A ARG* 3.2 56.5 + - - +
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Residues in contact with LEU 261 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO* 3.9 37.9 - - + +
217A PRO* 4.4 9.9 - - + -
224A PHE* 4.0 18.4 - - + -
253A PHE 3.7 32.8 - - - +
254A ASP* 3.8 13.9 - - - +
255A GLY* 4.1 5.9 - - - +
257A ASN 3.1 10.6 + - - +
258A LEU* 3.1 14.3 + - + +
260A GLU* 1.3 80.0 - - - +
262A ARG* 1.3 65.5 + - - +
264A ARG* 3.1 1.4 + - - +
265A VAL* 3.0 37.1 + - + +
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Residues in contact with ARG 262 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A PHE* 3.5 56.7 + - + -
258A LEU 2.8 15.4 + - - +
259A LYS* 3.4 19.2 + - - +
261A LEU* 1.3 72.8 - - - +
263A GLU* 1.3 56.9 + - - +
265A VAL* 3.1 1.8 + - - +
266A LEU* 2.7 55.9 + - + +
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Residues in contact with GLU 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A LYS* 2.8 20.3 + - - +
260A GLU* 3.7 11.3 - - + +
262A ARG* 1.3 75.9 - - - +
264A ARG* 1.3 64.3 + - + +
266A LEU* 4.2 5.2 - - - +
267A ARG* 3.2 26.2 + - + +
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Residues in contact with ARG 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A PHE* 3.3 25.2 - - + +
254A ASP* 2.7 42.2 + - - +
255A GLY* 3.5 1.2 - - - -
260A GLU* 3.2 50.8 + - - +
261A LEU 3.1 5.1 + - - +
263A GLU* 1.3 77.3 - - + +
265A VAL* 1.3 66.1 + - - +
267A ARG* 3.5 11.2 + - - +
268A GLY 3.0 17.2 + - - -
269A LYS 4.2 4.7 + - - +
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Residues in contact with VAL 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A PRO 5.0 2.5 - - - +
217A PRO 5.1 1.8 - - - +
219A ALA 4.1 11.9 - - - +
221A PRO* 3.8 30.9 - - + +
224A PHE* 4.5 11.9 - - + -
237A TRP* 4.0 15.2 - - + -
253A PHE* 3.6 29.6 - - + -
261A LEU* 3.0 37.4 + - + +
262A ARG 3.7 2.9 - - - +
264A ARG* 1.3 77.2 - - - +
266A LEU* 1.3 58.5 + - - +
268A GLY* 3.1 20.1 + - - -
290A LEU* 3.5 8.0 - - - +
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Residues in contact with LEU 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221A PRO* 3.6 30.3 - - + +
224A PHE* 4.0 12.6 - - + +
225A GLN* 3.8 28.0 - - + +
262A ARG* 2.7 53.2 + - + +
263A GLU* 4.2 4.7 - - - +
265A VAL* 1.3 70.3 - - - +
267A ARG* 1.3 64.1 + - - +
290A LEU* 3.3 21.1 - - - +
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Residues in contact with ARG 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A GLU* 3.2 20.4 + - + +
264A ARG* 3.8 11.0 - - - +
266A LEU* 1.3 76.4 - - - +
268A GLY* 1.3 61.6 + - - +
269A LYS* 3.3 27.7 + - + +
290A LEU* 3.7 11.8 - - - +
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Residues in contact with GLY 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A TRP* 4.8 2.7 - - - -
253A PHE* 3.8 12.9 - - - -
264A ARG 3.0 11.0 + - - -
265A VAL 3.1 14.3 + - - -
267A ARG* 1.3 77.6 - - - +
269A LYS* 1.3 58.0 + - - +
270A TYR* 3.3 19.6 - - - -
288A LEU* 4.9 5.9 - - - +
290A LEU* 3.7 15.1 - - - +
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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