Contacts of the helix formed by residues 251 - 262 (chain A) in PDB entry 1NNF
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 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A GLN* 5.7 0.4 - - - -
247A ASP 3.0 12.0 + - - -
248A PHE* 2.6 31.0 + - - -
250A ALA* 1.3 82.5 - - - +
252A LYS* 1.3 64.5 + - - +
253A LYS* 3.5 6.4 + - - +
254A GLY 3.1 11.3 + - - -
255A GLN* 2.9 22.5 + - - +
268A ARG* 3.5 5.8 - - - +
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Residues in contact with LYS 252 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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251A SER* 1.3 73.3 - - - +
253A LYS* 1.3 56.8 + - - +
255A GLN* 3.7 1.7 - - - +
256A GLU* 2.9 55.2 + - - +
268A ARG* 3.3 26.5 - - - +
270A ASP* 3.5 36.8 - - - +
271A VAL* 3.9 11.3 - - + +
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Residues in contact with LYS 253 (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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19A ALA* 5.0 2.6 - - - +
22A GLN* 2.5 39.7 - - - +
23A GLU* 2.7 40.0 + - + +
248A PHE* 4.0 13.1 - - + -
251A SER* 3.2 8.7 + - - +
252A LYS* 1.3 80.4 - - - +
254A GLY* 1.3 61.4 + - - +
256A GLU* 3.4 16.3 + - - +
257A ALA* 3.1 22.3 + - - +
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Residues in contact with GLY 254 (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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16A VAL* 4.0 5.9 - - - +
248A PHE* 3.1 38.7 - - - -
249A LEU* 4.0 7.8 - - - -
251A SER* 3.1 10.9 + - - -
253A LYS* 1.3 76.9 - - - +
255A GLN* 1.3 60.3 + - - +
257A ALA* 3.3 4.3 + - - +
258A LEU* 3.1 22.0 + - - +
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Residues in contact with GLN 255 (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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82A THR* 4.2 4.1 - - - +
98A LEU* 2.9 35.5 + - - +
99A SER* 5.3 0.8 - - - -
249A LEU 3.2 18.5 + - - +
250A ALA 4.1 1.3 - - - +
251A SER 2.9 20.5 + - - +
252A LYS 3.7 3.4 - - - +
254A GLY* 1.3 71.4 - - - +
256A GLU* 1.3 64.4 + - - +
258A LEU* 3.2 10.8 + - - +
259A VAL* 3.0 29.0 + - - +
266A PRO* 3.4 9.2 - - + +
267A LEU 3.0 26.0 + - - -
268A ARG* 3.1 24.7 + - + -
271A VAL* 3.8 18.4 - - + -
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Residues in contact with GLU 256 (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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252A LYS* 2.9 47.7 + - - +
253A LYS* 3.6 18.9 - - - +
254A GLY 3.3 0.2 - - - -
255A GLN* 1.3 76.8 - - - +
257A ALA* 1.3 61.3 + - - +
259A VAL* 3.4 9.9 - - + +
260A ALA* 3.2 24.9 + - - +
270A ASP 5.1 0.7 - - - +
271A VAL* 4.0 17.4 - - + +
272A VAL 5.8 1.1 - - - +
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Residues in contact with ALA 257 (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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15A ALA* 4.1 14.0 - - + +
16A VAL* 4.3 8.1 - - - -
19A ALA* 3.6 31.6 - - + -
253A LYS 3.1 10.7 + - - +
254A GLY* 3.5 9.9 - - - +
255A GLN 3.2 0.2 - - - -
256A GLU* 1.3 76.2 - - - +
258A LEU* 1.3 66.1 + - - +
260A ALA* 3.5 5.4 + - - +
261A ALA* 3.4 19.9 + - - +
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Residues in contact with LEU 258 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A GLN* 5.1 6.5 - - - +
12A ALA* 3.9 23.6 - - + -
16A VAL* 3.8 12.1 - - + +
55A TYR* 3.7 21.5 - - - +
98A LEU* 6.3 1.8 - - + -
99A SER* 3.9 32.1 - - - +
254A GLY 3.1 13.4 + - - +
255A GLN* 3.2 13.9 + - - +
257A ALA* 1.3 76.6 - - - +
259A VAL* 1.3 70.4 + - + +
261A ALA* 3.0 18.1 + - - -
262A ARG* 3.0 16.9 + - + +
264A GLU* 4.0 15.7 - - + -
266A PRO* 5.7 0.7 - - + -
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Residues in contact with VAL 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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255A GLN* 3.0 20.4 + - - +
256A GLU* 3.4 18.2 - - + +
258A LEU* 1.3 81.6 - - + +
260A ALA* 1.3 63.3 + - - +
262A ARG 3.3 8.4 - - - +
264A GLU 3.7 8.7 - - - +
266A PRO* 3.6 41.5 - - + -
271A VAL* 3.9 11.2 - - + -
272A VAL 4.0 2.2 - - - +
273A SER* 3.9 13.5 - - - +
274A PRO* 3.5 18.5 - - + +
275A PHE* 3.2 26.7 - - - -
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Residues in contact with ALA 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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256A GLU 3.2 18.4 + - - +
257A ALA* 3.9 6.7 - - - +
258A LEU 3.2 0.2 - - - -
259A VAL* 1.3 77.5 - - - +
261A ALA* 1.3 59.6 + - - +
274A PRO* 3.6 18.9 - - + +
275A PHE* 3.8 11.0 - - - -
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Residues in contact with ALA 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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11A GLU* 4.2 13.0 - - - +
12A ALA* 4.0 15.5 - - - +
15A ALA* 3.4 32.3 - - + -
257A ALA 3.4 2.2 + - - +
258A LEU 3.0 8.6 + - - +
260A ALA* 1.3 81.0 - - - +
262A ARG* 1.3 60.2 + - - +
275A PHE* 4.3 6.0 - - - -
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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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8A GLN* 4.0 7.8 + - - -
9A GLN* 3.6 20.3 - - - +
12A ALA* 4.1 26.5 - - + +
101A ARG* 3.5 23.0 - - - +
195A TYR* 3.6 20.2 - - + -
199A ASN* 5.3 6.0 + - - +
258A LEU* 3.0 13.4 + - + +
259A VAL* 3.3 16.3 - - - +
260A ALA 3.6 1.2 - - - -
261A ALA* 1.3 79.9 - - - +
263A ALA* 1.3 60.6 + - - +
264A GLU* 2.8 44.0 + - + +
273A SER* 5.2 0.2 + - - -
275A PHE* 3.6 7.9 - - - -
400A EDT 3.2 45.7 + - - -
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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