Contacts of the strand formed by residues 586 - 594 (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 TYR 586 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144A TRP* 5.2 1.2 - - - -
145A GLY* 3.3 2.3 - - - -
146A SER* 2.7 47.6 + - - +
564A LYS 3.4 3.8 - - - +
565A ILE* 4.0 29.4 - - + -
584A ARG* 2.8 43.0 + - + -
585A GLU* 1.3 74.4 - - - +
587A THR* 1.3 60.3 + - - +
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Residues in contact with THR 587 (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* 5.5 2.9 - - + +
40A THR* 5.7 5.6 - - + -
144A TRP 3.9 9.4 - - - +
145A GLY* 3.9 8.9 - - - -
149A TYR* 4.4 19.1 - - + -
563A GLY* 3.7 1.7 - - - -
564A LYS* 2.9 54.8 + - - +
585A GLU* 4.0 8.5 + - - +
586A TYR* 1.3 76.7 + - - +
588A LEU* 1.3 70.5 + - - +
589A SER* 5.2 6.5 - - - -
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Residues in contact with LEU 588 (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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144A TRP* 2.9 47.1 + - + +
561A VAL* 4.4 15.7 - - + -
562A ARG 2.9 19.7 - - - +
563A GLY* 3.7 12.8 - - - -
587A THR* 1.3 73.6 - - - +
589A SER* 1.3 71.3 + - - +
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Residues in contact with SER 589 (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* 4.7 6.2 - - - +
142A ALA 3.4 13.9 - - - -
143A GLY* 4.2 5.6 - - - -
561A VAL* 3.5 6.2 - - - +
562A ARG* 2.7 60.6 + - - +
587A THR* 5.2 7.2 - - - -
588A LEU* 1.3 84.1 - - - +
590A GLY* 1.3 58.9 + - - +
591A SER* 5.5 0.3 + - - -
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Residues in contact with GLY 590 (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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141A SER* 3.3 3.8 - - - -
142A ALA* 3.0 30.9 + - - +
559A LEU* 5.8 1.1 - - - -
560A THR 3.2 9.9 - - - -
561A VAL* 4.4 3.8 - - - -
562A ARG* 5.6 0.4 - - - -
589A SER* 1.3 79.4 + - - +
591A SER* 1.3 67.7 + - - -
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Residues in contact with SER 591 (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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139A GLU* 4.5 17.1 + - - -
140A ILE 3.9 5.8 - - - -
141A SER* 4.0 12.2 - - - -
559A LEU* 2.9 9.6 + - - +
560A THR* 2.8 44.9 + - - -
562A ARG* 4.7 14.6 + - - -
589A SER* 5.5 0.3 + - - -
590A GLY* 1.3 77.4 + - - -
592A TYR* 1.3 61.2 + - - +
593A THR* 5.2 2.2 - - - -
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Residues in contact with TYR 592 (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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138A THR 4.1 0.3 - - - +
139A GLU* 3.5 4.3 - - - -
140A ILE* 3.1 41.2 + - + +
558A HIS* 2.6 37.0 + + + -
559A LEU* 4.2 10.3 - - + -
591A SER* 1.3 74.6 - - - +
593A THR* 1.3 67.0 + - - +
594A PHE* 3.1 50.9 - + + +
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Residues in contact with THR 593 (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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137A GLY* 5.5 4.3 - - - -
138A THR 3.6 13.2 - - - +
139A GLU* 3.7 20.1 + - + +
558A HIS* 2.3 49.4 - - + +
559A LEU 5.6 0.2 + - - -
591A SER* 5.2 2.4 + - - -
592A TYR* 1.3 81.1 + - - +
594A PHE* 1.3 73.7 + - - +
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Residues in contact with PHE 594 (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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137A GLY* 3.8 8.7 - - - -
138A THR* 3.2 59.3 + - + +
140A ILE* 4.1 28.5 - - + -
558A HIS* 4.4 9.4 - - + -
592A TYR* 3.1 43.7 - + + +
593A THR* 1.3 81.1 - - - +
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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