Contacts of the strand formed by residues 302 - 310 (chain A) in PDB entry 3NKO
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 VAL 302 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A LEU* 3.3 11.9 - - + +
167A ILE* 3.9 16.4 - - + -
259A LEU* 4.2 4.3 - - + -
260A TRP* 5.7 0.4 - - - -
263A ALA* 4.6 10.8 - - + -
268A VAL* 5.1 1.1 - - + -
269A ARG 4.0 2.7 - - - +
270A ALA* 3.6 27.1 - - + +
271A GLY 2.7 32.1 + - - -
273A PHE* 3.7 23.6 - - + -
300A PRO* 4.0 0.9 - - - +
301A SER* 1.3 81.4 - - - +
303A TYR* 1.3 64.7 + - - +
516A LEU* 3.9 29.8 - - + -
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Residues in contact with TYR 303 (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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164A PRO* 4.2 3.4 - - + -
165A LEU 2.9 16.0 + - - +
166A ILE* 3.4 20.6 - - + -
167A ILE* 2.8 31.2 + - - +
271A GLY* 4.7 4.7 - - - +
273A PHE* 4.7 1.3 - - - -
288A ILE* 3.9 31.2 - - + -
291A TRP* 3.7 39.4 + + + -
292A LEU* 3.4 29.6 - - + +
299A ARG* 3.5 5.9 - - - +
300A PRO* 2.6 56.1 + - + +
301A SER 3.9 6.3 - - - -
302A VAL* 1.3 80.0 - - - +
304A ALA* 1.3 61.6 + - - +
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Residues in contact with ALA 304 (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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166A ILE* 5.6 0.2 - - - -
167A ILE* 3.3 7.2 - - + +
272A THR 3.7 20.6 + - - +
273A PHE* 3.8 29.8 - - + -
275A TRP* 2.9 27.7 + - - +
288A ILE* 3.8 6.3 - - - +
291A TRP* 5.9 0.6 - - - -
303A TYR* 1.3 77.2 - - - +
305A PHE* 1.3 59.7 + - - +
1006A NKO 4.0 19.5 - - + -
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Residues in contact with PHE 305 (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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166A ILE* 5.3 2.9 - - + +
167A ILE 2.8 10.8 + - - +
168A PHE* 3.3 49.1 - + + -
169A SER* 2.9 28.2 + - - -
275A TRP* 3.9 3.1 - - - +
281A HIS* 3.9 16.6 - + + -
284A ARG* 3.9 34.1 - - + -
285A ILE* 3.5 24.2 - - + -
288A ILE* 3.9 12.6 - - + -
304A ALA* 1.3 76.5 - - - +
306A TYR* 1.3 79.7 + - - +
307A SER* 3.7 8.3 - - - -
334A THR* 3.7 15.0 - - + -
338A LEU* 6.0 0.4 - - + -
1006A NKO 4.3 2.2 - - - +
1025A EDO 3.9 8.3 - - - -
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Residues in contact with TYR 306 (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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169A SER* 3.5 15.7 - - - -
170A VAL 5.2 0.4 - - - -
171A ASP* 2.6 35.0 + - + -
213A LEU* 4.2 18.8 - - + -
275A TRP* 4.0 9.6 - - + -
281A HIS* 4.2 0.2 + - - -
284A ARG* 2.8 34.5 + - - -
305A PHE* 1.3 87.3 - - - +
307A SER* 1.3 77.4 + - - +
308A GLU* 3.6 18.8 - - + +
1006A NKO 3.1 88.9 + - + +
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Residues in contact with SER 307 (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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169A SER 3.0 11.6 + - - -
170A VAL* 4.3 8.5 - - - -
171A ASP* 3.0 29.3 + - - +
281A HIS* 3.1 24.4 - - - -
305A PHE* 3.7 13.2 - - - -
306A TYR* 1.3 81.4 - - - +
308A GLU* 1.3 61.0 + - - +
309A GLN 3.1 20.8 + - - -
331A ILE* 5.0 0.4 - - - -
1025A EDO 3.4 13.4 - - - -
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Residues in contact with GLU 308 (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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171A ASP* 3.8 2.2 - - - -
281A HIS* 2.8 36.1 + - - -
284A ARG* 4.3 11.1 + - - -
306A TYR* 3.6 25.3 - - + +
307A SER* 1.3 73.3 + - - +
309A GLN* 1.3 69.9 + - + +
311A ASP* 3.3 23.9 - - - +
312A PHE* 3.4 15.8 + - + +
1006A NKO 4.3 13.8 - - - +
1025A EDO 5.0 0.5 + - - -
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Residues in contact with GLN 309 (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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170A VAL* 3.9 1.4 - - - +
171A ASP 3.3 15.7 + - - -
307A SER* 3.1 21.9 + - - +
308A GLU* 1.3 90.3 - - + +
310A PRO* 1.3 74.1 - - + +
311A ASP 3.3 3.4 - - - -
312A PHE* 3.4 15.8 + - + +
313A SER* 2.9 46.2 + - - +
327A PRO* 3.9 14.4 - - + +
330A GLU* 5.7 3.4 + - - -
331A ILE* 3.5 10.8 - - + +
1025A EDO 3.8 22.7 - - - +
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Residues in contact with PRO 310 (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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170A VAL* 4.4 1.1 - - + -
171A ASP 3.0 11.7 - - - +
172A GLY 3.8 17.8 - - - +
173A PHE* 3.8 23.3 - - + +
177A TYR* 3.8 13.2 + - + -
309A GLN* 1.3 90.5 - - + +
311A ASP* 1.3 56.5 + - - +
313A SER 3.4 1.9 + - - -
314A GLY* 2.8 26.3 + - - -
324A MET* 3.6 21.9 - - + +
327A PRO* 4.6 4.9 - - + -
328A LEU* 4.0 9.9 - - + -
331A ILE* 3.4 18.2 - - + -
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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