Contacts of the strand formed by residues 655 - 660 (chain A) in PDB entry 2NUP
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 GLN 655 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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650A MET* 3.5 5.0 - - + +
651A ASP* 3.9 0.2 - - - -
652A THR* 2.6 66.0 + - + +
653A PHE 3.4 0.4 + - - -
654A PHE* 1.3 76.6 - - + +
656A ILE* 1.3 64.7 + - - +
657A LEU* 4.3 7.5 - - + +
703A PRO* 3.8 2.5 - - - -
704A ARG* 3.2 23.7 + - + +
706A ILE* 3.4 25.7 - - + +
717A PHE* 3.2 45.0 + - - +
721A LYS* 4.9 8.1 - - - +
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Residues in contact with ILE 656 (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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649A LEU* 3.8 20.4 - - + -
650A MET 3.5 2.7 - - - -
651A ASP* 4.6 8.7 - - + +
655A GLN* 1.3 75.3 - - - +
657A LEU* 1.3 62.0 + - - +
692A ALA* 4.0 20.0 - - + +
695A ILE* 3.3 34.1 - - + -
696A LEU* 3.8 22.2 - - + +
699A ARG* 4.3 11.0 - - - +
703A PRO* 3.8 20.1 - - + +
704A ARG 2.9 8.0 + - - +
705A TYR* 3.4 17.5 - - + -
706A ILE* 3.0 24.8 + - - +
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Residues in contact with LEU 657 (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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648A LEU 3.7 0.5 - - - +
649A LEU* 3.3 5.2 - - - +
650A MET* 2.7 58.2 + - + +
655A GLN* 4.0 10.1 + - - +
656A ILE* 1.3 74.8 - - - +
658A ILE* 1.3 81.5 + - - +
659A TYR* 4.0 9.6 - - + +
706A ILE* 3.6 26.7 - - + -
708A THR* 3.8 11.0 - - + -
714A GLN 4.0 8.5 - - - +
717A PHE* 3.5 33.2 - - + -
718A LEU* 4.2 18.8 - - + +
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Residues in contact with ILE 658 (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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647A ILE* 3.7 24.5 - - + -
648A LEU 3.1 4.0 - - - +
649A LEU* 4.3 9.6 - - + -
656A ILE* 5.3 0.2 - - + -
657A LEU* 1.3 84.2 - - - +
659A TYR* 1.3 63.0 + - - +
660A HIS* 3.8 19.1 - - + +
688A PRO* 3.7 15.5 - - + +
689A VAL* 3.7 31.9 - - + +
692A ALA* 4.6 0.9 - - + -
705A TYR* 3.0 36.6 - - + +
706A ILE 3.0 11.8 + - - +
707A ASP* 4.9 5.6 - - - +
708A THR* 3.2 26.2 + - - +
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Residues in contact with TYR 659 (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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642A ILE* 3.5 29.0 - - + +
643A LEU 4.7 2.0 - - - -
646A ARG 4.8 3.4 - - - -
647A ILE* 3.1 12.1 - - - +
648A LEU* 2.8 45.5 + - + -
657A LEU* 4.0 4.7 - - + +
658A ILE* 1.3 74.4 - - - +
660A HIS* 1.3 62.8 + - - +
661A GLY* 3.5 23.3 - - - -
708A THR* 3.8 11.9 - - + -
709A GLU* 3.6 9.4 - - - -
710A HIS* 3.0 49.5 + - - +
715A ALA* 3.9 15.7 - - + -
718A LEU* 3.6 31.9 - - + -
719A LEU* 5.7 5.1 - - + +
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Residues in contact with HIS 660 (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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646A ARG 4.3 1.8 - - - -
647A ILE* 3.2 47.6 - - + +
658A ILE* 3.8 14.1 - - + +
659A TYR* 1.3 77.4 - - - +
661A GLY* 1.3 68.0 + - - +
664A ILE* 4.1 5.9 - - + +
665A ALA* 4.1 15.2 - - - +
685A LEU* 3.4 27.9 + - + +
707A ASP* 3.9 20.5 + - - -
708A THR 3.4 21.7 + - - -
709A GLU* 3.1 30.5 - - + +
710A HIS 3.2 5.7 + - - -
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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