Contacts of the helix formed by residues 646 - 653 (chain N) in PDB entry 5X22
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 LYS 646 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188L GLN* 3.4 23.0 - - - +
644N LEU 3.5 1.9 + - - -
645N PRO* 1.3 69.3 - - - +
647N ARG* 1.3 64.4 + - + +
649N ALA* 2.9 9.7 + - - +
650N LEU* 2.9 28.9 + - - +
688N TRP* 3.5 47.0 - - + +
691N LEU* 4.2 0.3 - - - +
692N GLU* 5.6 2.5 - - - +
720N LEU* 4.2 17.9 - - + -
721N VAL 3.1 25.9 + - - +
722N GLU* 3.1 40.8 + - - +
723N GLY 4.6 1.2 + - - -
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Residues in contact with ARG 647 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
795M GLY* 6.5 0.9 - - - -
1005M MET* 4.2 25.9 - - + +
1007M ALA* 5.0 0.5 - - - +
645N PRO* 3.3 1.5 - - + +
646N LYS* 1.3 83.7 - - + +
648N MET* 1.3 62.8 + - - +
650N LEU* 3.7 32.5 - - - +
651N GLU* 3.9 7.6 + - - +
680N GLN* 3.7 42.1 + - - +
683N ILE* 4.3 11.3 - - - +
688N TRP* 3.7 24.5 - - + -
723N GLY 5.6 4.5 - - - +
724N GLN* 5.9 5.8 - - + -
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Residues in contact with MET 648 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1005M MET* 3.8 26.7 - - + -
1006M HIS 3.6 21.8 - - - +
1007M ALA* 3.8 8.6 - - + +
627N GLY* 4.1 6.3 - - - -
628N ARG 4.0 8.3 - - - +
629N SER* 3.7 28.0 - - - -
644N LEU* 4.4 7.0 - - + -
645N PRO* 3.3 24.9 + - + +
646N LYS 3.1 0.6 - - - -
647N ARG* 1.3 75.9 - - - +
649N ALA* 1.3 60.0 + - - +
650N LEU 3.1 2.0 - - - -
651N GLU* 3.0 6.2 + - - +
652N LEU* 2.9 38.5 + - + +
726N ILE* 4.3 2.2 - - - -
747N VAL* 3.7 30.1 - - + -
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Residues in contact with ALA 649 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644N LEU* 3.9 16.1 - - + +
645N PRO 3.2 5.6 + - - +
646N LYS 2.9 8.6 + - - +
648N MET* 1.3 75.7 - - - +
650N LEU* 1.3 64.4 + - - +
652N LEU* 3.9 3.1 - - - -
653N PHE* 3.1 40.6 + - + +
691N LEU* 3.8 12.7 - - + +
695N ILE* 5.4 0.4 - - + -
720N LEU* 3.6 29.2 - - + -
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Residues in contact with LEU 650 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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646N LYS 2.9 10.8 + - - +
647N ARG* 3.7 19.7 - - - +
648N MET 3.1 0.2 - - - -
649N ALA* 1.3 78.1 - - - +
651N GLU* 1.3 61.0 + - + +
653N PHE 4.0 0.3 - - - -
654N LYS* 3.2 35.7 + - - +
657N LEU* 4.1 15.6 - - + +
677N LEU* 3.7 35.4 - - + +
683N ILE* 3.9 24.0 - - + -
687N VAL* 5.7 1.6 - - + -
688N TRP* 3.5 31.9 - - + -
691N LEU* 3.9 7.6 - - - +
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Residues in contact with GLU 651 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007M ALA* 3.6 28.5 - - + +
1008M ARG* 3.6 1.3 - - - -
1009M SER* 2.9 61.5 + - - +
1010M THR 4.5 0.5 - - - +
1027M PHE* 3.5 21.1 - - + -
647N ARG 3.9 5.6 + - - +
648N MET 3.0 7.7 + - - +
650N LEU* 1.3 80.1 - - - +
652N LEU* 1.3 65.4 + - - +
654N LYS* 2.9 37.3 + - - +
674N ARG* 5.4 0.9 + - - -
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Residues in contact with LEU 652 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1007M ALA* 4.1 8.5 - - + -
1008M ARG 4.0 5.8 - - - +
625N TYR* 3.5 29.5 - - - +
626N SER* 3.4 45.5 - - - +
627N GLY 3.8 1.1 - - - +
644N LEU* 4.4 13.5 - - + -
648N MET* 2.9 35.2 + - + +
651N GLU* 1.3 78.1 - - - +
653N PHE* 1.3 67.4 + - + +
654N LYS 3.6 0.3 + - - -
655N PRO* 4.5 0.3 - - - +
656N PHE* 5.2 1.7 - - - -
747N VAL* 3.8 31.2 - - + +
749N VAL* 3.9 20.3 - - + +
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Residues in contact with PHE 653 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644N LEU* 4.3 15.5 - - + -
649N ALA* 3.1 28.3 + - + +
650N LEU 4.0 1.1 - - - -
652N LEU* 1.3 76.1 - - + +
654N LYS* 1.3 65.8 + - - +
655N PRO* 3.3 4.7 - - - -
656N PHE* 2.9 36.8 + + + +
657N LEU* 3.0 9.2 + - - -
691N LEU* 4.1 11.7 - - + -
694N VAL* 4.4 8.7 - - + -
695N ILE* 3.6 33.0 - - + -
698N LYS* 4.7 20.2 - - + -
699N VAL 5.4 1.3 - - - -
700N VAL* 3.6 31.2 - - + -
718N PRO* 5.1 2.9 - - + -
749N VAL* 3.6 28.9 - - + -
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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