Contacts of the strand formed by residues 560 - 565 (chain A) in PDB entry 1NQF
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 THR 560 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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552A ALA* 4.7 3.4 - - + -
553A TYR 3.2 24.2 - - - +
554A PRO* 4.2 9.2 - - + +
555A VAL 4.5 1.1 - - - +
557A SER 5.1 4.3 + - - -
559A LEU* 1.3 77.1 + - - +
561A VAL* 1.3 71.3 + - - +
562A ARG* 4.4 29.4 + - + +
590A GLY* 3.2 4.7 - - - -
591A SER* 2.8 42.6 + - - -
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Residues in contact with VAL 561 (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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552A ALA* 3.5 1.4 - - - -
553A TYR* 2.8 37.6 + - + +
555A VAL* 4.1 16.8 - - + -
559A LEU* 3.9 22.4 - - + +
560A THR* 1.3 77.2 - - - +
562A ARG* 1.3 65.9 + - - +
588A LEU* 4.4 17.3 - - + -
589A SER 3.5 9.6 - - - +
590A GLY* 4.4 1.8 - - - -
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Residues in contact with ARG 562 (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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35A ASP* 3.0 52.2 + - - +
36A ARG* 3.8 13.1 - - - +
38A GLN* 3.5 25.1 - - - +
515A ASP* 5.4 0.2 + - - -
551A VAL* 3.3 4.7 - - - -
552A ALA* 3.7 22.4 - - + +
560A THR* 4.4 21.6 + - + +
561A VAL* 1.3 82.6 - - - +
563A GLY* 1.3 60.2 + - - +
588A LEU* 2.9 20.8 - - - +
589A SER* 2.7 38.9 + - - +
590A GLY* 5.8 0.2 - - - -
591A SER* 4.7 14.5 + - - -
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Residues in contact with GLY 563 (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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38A GLN* 2.9 8.4 - - - +
549A LEU 4.0 0.3 - - - +
550A ALA* 3.3 1.0 - - - -
551A VAL* 2.7 54.9 + - - +
562A ARG* 1.3 77.0 - - - +
564A LYS* 1.3 57.6 + - - -
587A THR 3.7 5.8 - - - -
588A LEU* 3.7 8.7 - - - -
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Residues in contact with LYS 564 (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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37A TRP 3.7 9.5 + - - +
38A GLN* 3.0 41.8 + - + +
39A SER* 4.8 0.2 - - - +
40A THR* 5.6 2.4 + - - +
44A ASP* 3.8 19.0 + - - -
47A ARG* 5.5 0.2 - - - +
48A ARG* 4.4 4.8 - - - +
548A ASP* 4.8 11.9 - - - -
549A LEU 3.4 10.1 - - - +
550A ALA* 4.4 6.3 - - + -
563A GLY* 1.3 74.4 - - - +
565A ILE* 1.3 81.8 - - - +
566A ALA* 4.2 23.3 - - + +
586A TYR* 3.4 5.4 - - - +
587A THR* 2.9 54.9 + - - +
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Residues in contact with ILE 565 (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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547A TRP 4.3 0.3 - - - +
548A ASP* 3.3 4.3 - - - -
549A LEU* 2.9 47.3 + - + +
563A GLY 5.9 0.2 - - - -
564A LYS* 1.3 85.2 - - - +
566A ALA* 1.3 66.7 + - - +
568A LEU* 3.6 32.8 + - + -
584A ARG* 4.3 14.4 - - - +
585A GLU 3.5 7.6 - - - +
586A TYR* 4.0 24.2 - - + -
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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