Contacts of the strand formed by residues 1257 - 1263 (chain D) in PDB entry 5NPK
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 GLN1257 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1249D ILE* 3.6 23.1 - - + +
1250D GLU 3.1 13.9 - - - +
1251D GLU* 3.1 30.0 + - - +
1252D ARG* 3.3 10.2 + - - -
1255D GLY 4.0 4.0 + - - +
1256D ARG* 1.3 76.0 - - - +
1258D ARG* 1.3 63.0 + - - +
1308D VAL* 3.2 30.5 + - + +
1310D LYS* 5.9 0.4 - - - +
1312D ALA 4.6 5.4 - - - +
1314D ALA* 3.8 23.0 + - + +
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Residues in contact with ARG1258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248D VAL 3.6 0.5 - - - +
1249D ILE* 3.3 6.0 - - - +
1250D GLU* 2.8 68.2 + - + +
1251D GLU 5.7 0.9 - - - -
1252D ARG* 4.0 26.1 - - + +
1257D GLN* 1.3 78.2 - - - +
1259D ILE* 1.3 64.0 + - - +
1260D VAL* 3.7 9.3 + - + +
1293D ARG* 4.8 9.3 - - - +
1303D ARG* 3.3 23.7 - - - +
1305D VAL* 3.7 14.3 - - + +
1306D ILE 3.4 8.7 - - - +
1307D ASP* 3.3 25.1 + - - +
1308D VAL* 4.2 3.6 - - - -
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Residues in contact with ILE1259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1247D ALA* 4.1 10.3 - - + -
1248D VAL 3.4 8.3 - - - +
1249D ILE* 4.2 15.9 - - + -
1258D ARG* 1.3 76.1 - - - +
1260D VAL* 1.3 62.8 + - - +
1261D VAL* 4.2 3.4 - - + -
1304D VAL 3.5 3.5 - - - +
1305D VAL* 3.5 1.7 - - - +
1306D ILE* 2.8 60.9 + - + +
1308D VAL* 4.4 16.8 - - + -
1314D ALA* 3.8 20.0 - - + +
1317D ILE* 4.5 5.4 - - + -
1318D LEU* 3.7 43.1 - - + +
1321D LEU* 4.3 11.4 - - + -
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Residues in contact with VAL1260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246D ARG 4.0 0.2 - - - +
1247D ALA* 3.4 2.0 - - - -
1248D VAL* 2.9 47.4 + - + +
1250D GLU* 3.6 31.0 - - - +
1258D ARG* 3.7 18.4 - - + +
1259D ILE* 1.3 77.6 - - - +
1261D VAL* 1.3 61.0 + - - +
1262D THR* 3.9 18.9 + - + +
1303D ARG* 3.5 40.8 - - + +
1304D VAL 3.5 3.4 - - - +
1305D VAL* 4.7 4.7 - - + -
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Residues in contact with VAL1261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1245D SER* 3.9 11.2 - - - -
1246D ARG 3.4 7.2 - - - +
1247D ALA* 4.0 16.6 - - + -
1259D ILE* 4.2 11.0 - - + -
1260D VAL* 1.3 73.4 - - - +
1262D THR* 1.3 59.7 + - - +
1263D GLU 3.4 23.1 - - - +
1264D ILE* 3.9 16.2 - - + -
1273D MET* 5.1 0.4 - - + -
1302D VAL* 3.7 2.3 - - - +
1303D ARG* 3.2 6.6 + - - -
1304D VAL* 2.8 53.7 + - + +
1306D ILE* 4.2 10.8 - - + -
1327D LEU* 4.0 20.4 - - + -
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Residues in contact with THR1262 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1246D ARG* 3.1 28.0 + - - +
1248D VAL* 5.9 2.9 - - + -
1260D VAL* 3.9 21.1 + - + +
1261D VAL* 1.3 77.7 - - - +
1263D GLU* 1.3 68.4 + - - +
1300D THR* 6.3 0.7 - - + -
1302D VAL* 3.2 36.0 + - - +
1303D ARG* 4.9 5.2 - - + +
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Residues in contact with GLU1263 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1220D THR 3.9 5.2 - - - +
1221D ALA* 3.5 21.9 - - + +
1222D GLY* 2.7 37.2 + - - +
1245D SER* 3.1 8.8 - - - -
1246D ARG* 3.0 62.7 + - + -
1261D VAL* 3.4 4.2 - - - +
1262D THR* 1.3 85.7 + - - +
1264D ILE* 1.3 66.0 + - - +
1302D VAL* 4.8 3.1 - - - -
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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