Contacts of the strand formed by residues 1328 - 1334 (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 GLN1328 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1225D LEU* 3.4 23.4 - - - +
1242D GLN* 3.3 26.3 + - - +
1243D MET 3.3 14.6 - - - +
1244D ARG* 2.8 35.7 + - - +
1322D TYR* 3.4 34.4 + - + +
1325D THR 3.3 16.6 + - - +
1326D PRO* 3.9 0.5 - - - +
1327D LEU* 1.3 78.3 - - - +
1329D THR* 1.3 66.7 + - - +
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Residues in contact with THR1329 (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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1242D GLN* 4.4 5.4 - - - -
1243D MET* 2.8 64.4 + - + +
1265D PRO* 3.6 14.6 - - + +
1266D PHE 4.8 0.4 - - - +
1268D VAL* 3.8 12.4 - - + +
1326D PRO* 3.8 16.9 + - - +
1327D LEU 4.2 0.2 - - - -
1328D GLN* 1.3 77.6 + - - +
1330D SER* 1.4 60.5 + - - +
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Residues in contact with SER1330 (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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1240D SER* 4.0 9.5 + - - -
1241D ILE 3.1 7.4 - - - -
1242D GLN* 3.3 27.8 + - - +
1243D MET* 4.2 6.1 - - - +
1329D THR* 1.4 77.9 + - - +
1331D PHE* 1.3 61.7 + - - +
1332D GLY* 3.9 3.3 + - - -
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Residues in contact with PHE1331 (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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1182D ASN* 3.4 38.8 - - - +
1183D ILE 3.8 4.3 - - - -
1184D PRO* 3.6 42.8 - - + -
1218D PHE* 4.2 16.2 - + + -
1239D GLY 3.6 0.5 - - - +
1240D SER* 4.7 0.4 - - - -
1241D ILE* 2.6 42.6 + - + +
1243D MET* 4.1 19.1 - - + -
1266D PHE* 4.0 19.7 - + - -
1267D GLN* 3.8 20.4 - - - -
1329D THR 4.1 0.4 + - - -
1330D SER* 1.3 74.7 - - - +
1332D GLY* 1.3 59.8 + - - +
1333D VAL* 3.2 20.3 + - + +
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Residues in contact with GLY1332 (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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1182D ASN* 2.8 32.0 + - - +
1239D GLY 3.8 5.2 - - - -
1240D SER* 4.6 6.1 - - - -
1330D SER* 3.9 5.9 + - - -
1331D PHE* 1.3 71.2 - - - +
1333D VAL* 1.3 64.4 + - - -
1334D ASN* 4.4 2.0 - - - +
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Residues in contact with VAL1333 (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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1182D ASN 3.5 7.4 - - - +
1184D PRO* 4.1 11.7 - - + -
1233D ALA* 3.6 23.6 - - + -
1234D TYR* 6.2 1.1 - - + -
1237D GLY 3.7 3.8 - - - +
1238D ARG* 3.3 22.3 + - - +
1239D GLY 2.8 23.0 + - - +
1241D ILE* 3.7 27.1 - - + -
1331D PHE* 3.6 23.6 - - + +
1332D GLY* 1.3 74.3 - - - -
1334D ASN* 1.3 63.4 + - - +
1335D MET* 3.5 27.6 - - + -
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Residues in contact with ASN1334 (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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1180D ALA* 2.9 34.8 + - - +
1181D THR* 3.2 1.8 + - - +
1182D ASN* 2.8 41.3 + - + +
1237D GLY 3.4 3.1 - - - -
1238D ARG* 3.4 33.2 + - - +
1332D GLY 3.6 4.5 + - - +
1333D VAL* 1.3 77.6 - - - +
1335D MET* 1.3 59.7 + - - +
1336D ILE* 3.1 16.0 + - - +
1345D LEU* 3.9 8.1 - - - +
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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