Contacts of the helix formed by residues 639 - 656 (chain A) in PDB entry 6MZL
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 LEU 639 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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637A GLN 3.6 13.9 - - - +
638A PRO* 1.3 76.5 - - - +
640A LEU* 1.3 59.0 + - - +
641A LYS 3.3 2.7 - - - -
642A HIS* 2.9 30.8 + - + +
643A ILE* 2.9 35.1 + - + +
674A LYS* 3.4 35.4 - - + +
765A ILE* 5.5 0.4 - - + -
772A TYR* 3.6 32.5 - - + -
773A ILE 3.5 17.4 + - - +
774A ARG* 3.7 26.2 - - + -
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Residues in contact with LEU 640 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A PRO* 3.8 2.9 - - + +
639A LEU* 1.3 76.1 - - - +
641A LYS* 1.3 63.7 + - + +
643A ILE* 4.0 12.8 - - + +
644A LYS* 3.3 55.8 + - + +
32J VAL 4.5 6.1 - - - +
33J GLN* 4.0 16.2 - - - +
34J SER 4.1 4.3 - - - +
35J GLY* 3.7 34.1 + - - +
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Residues in contact with LYS 641 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LEU 3.3 0.4 - - - -
640A LEU* 1.3 78.6 - - + +
642A HIS* 1.3 63.3 + - - +
644A LYS* 3.6 5.4 + - - +
645A LYS* 3.1 25.1 + - - +
35J GLY 4.8 15.5 + - - +
36J HIS* 6.3 0.2 - - - +
37J VAL* 4.9 16.8 - - + -
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Residues in contact with HIS 642 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A PRO 5.7 0.7 - - - +
639A LEU* 2.9 26.9 + - + +
641A LYS* 1.3 78.1 - - - +
643A ILE* 1.3 63.8 + - - +
645A LYS* 3.6 6.5 + - - +
646A LYS* 3.1 41.1 + - - +
672A THR* 5.7 1.0 - - - +
674A LYS* 3.6 37.1 - - + +
675A ASP* 4.3 11.4 + - + +
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Residues in contact with ILE 643 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A LEU* 2.9 30.5 + - + +
640A LEU* 4.0 15.5 - - + +
641A LYS 3.4 0.2 - - - -
642A HIS* 1.3 77.2 - - - +
644A LYS* 1.3 60.6 + - + +
646A LYS* 3.4 2.0 + - - +
647A ALA* 3.0 31.6 + - + +
674A LYS 3.5 19.3 - - - +
675A ASP* 4.4 5.8 - - - +
676A GLY* 4.4 17.8 + - - +
677A ASP* 5.5 3.8 - - - +
774A ARG* 3.4 36.3 - - + +
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Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
640A LEU* 3.3 50.5 + - + +
641A LYS* 4.1 4.7 - - - +
643A ILE* 1.3 79.0 - - + +
645A LYS* 1.3 57.8 + - - +
647A ALA* 3.9 4.5 - - - +
648A LYS* 3.0 34.9 + - - +
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Residues in contact with LYS 645 (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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641A LYS 3.1 20.6 + - - +
642A HIS* 3.9 7.2 - - - +
643A ILE 3.3 0.2 - - - -
644A LYS* 1.3 77.4 - - - +
646A LYS* 1.3 57.0 + - - +
648A LYS* 3.4 21.4 + - + +
649A MET* 3.0 32.3 + - + +
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Residues in contact with LYS 646 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A HIS* 3.1 37.5 + - + +
643A ILE 4.0 1.1 - - - +
645A LYS* 1.3 75.3 - - - +
647A ALA* 1.3 61.4 + - - +
649A MET* 3.5 30.6 - - + +
650A ARG* 3.0 59.4 + - - +
670A ASP* 4.9 7.8 + - - +
675A ASP* 3.3 36.8 - - + +
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Residues in contact with ALA 647 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643A ILE* 3.0 22.6 + - + +
644A LYS* 4.0 4.7 - - - +
646A LYS* 1.3 73.5 - - - +
648A LYS* 1.3 63.7 + - - +
650A ARG* 4.1 6.4 - - - +
651A GLU* 3.1 24.3 + - - +
676A GLY* 6.0 4.9 - - - +
80J ILE* 6.4 1.6 - - - -
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Residues in contact with LYS 648 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A LYS* 3.0 22.5 + - - +
645A LYS* 3.6 23.8 - - + +
647A ALA* 1.3 78.1 - - - +
649A MET* 1.3 56.6 + - - +
651A GLU* 3.2 6.2 + - - +
652A GLN* 2.8 56.3 + - + +
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Residues in contact with MET 649 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A LYS* 3.0 22.3 + - + +
646A LYS* 3.5 40.2 - - + +
648A LYS* 1.3 75.9 - - - +
650A ARG* 1.3 62.3 + - + +
652A GLN* 3.2 13.5 + - - +
653A GLU* 2.8 35.4 + - + +
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Residues in contact with ARG 650 (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 LYS* 3.0 39.6 + - + +
647A ALA* 4.2 5.8 - - - +
649A MET* 1.3 80.1 - - + +
651A GLU* 1.3 57.9 + - - +
653A GLU* 3.5 6.2 + - - +
654A ARG* 3.0 21.9 + - - +
664A PHE* 3.4 49.3 - - + +
665A MET* 3.9 12.1 - - - +
670A ASP* 3.5 27.5 + - - +
675A ASP* 2.9 29.7 + - - -
676A GLY* 4.7 4.2 - - - -
78J LYS* 3.7 23.4 - - - +
80J ILE* 3.4 35.2 - - + +
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Residues in contact with GLU 651 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A ALA 3.1 20.9 + - - +
648A LYS* 3.5 6.3 - - - +
650A ARG* 1.3 76.0 - - - +
652A GLN* 1.3 57.9 + - + +
654A ARG* 3.2 34.6 + - - +
655A GLN* 3.0 56.1 + - + +
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Residues in contact with GLN 652 (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 LYS* 2.8 45.1 + - + +
649A MET* 3.2 11.7 + - + +
651A GLU* 1.3 74.5 - - + +
653A GLU* 1.3 60.1 + - - +
655A GLN* 3.4 5.3 + - - +
656A ALA* 3.0 31.0 + - - +
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Residues in contact with GLU 653 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A MET* 2.8 23.1 + - + +
650A ARG* 3.8 8.7 - - - +
652A GLN* 1.3 75.8 - - - +
654A ARG* 1.3 63.4 + - - +
656A ALA* 3.7 10.5 + - - +
657A SER* 3.8 14.3 + - - +
662A MET* 4.3 14.9 - - + +
664A PHE* 4.2 14.7 - - + -
666A ARG* 3.2 38.5 + - - -
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Residues in contact with ARG 654 (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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650A ARG 3.0 14.0 + - - +
651A GLU* 3.2 38.6 + - - +
653A GLU* 1.3 77.2 - - - +
655A GLN* 1.3 65.0 + - - +
656A ALA 3.4 0.5 + - - -
657A SER* 3.5 6.2 + - - -
658A GLY 3.3 0.5 + - - -
659A GLY* 2.8 34.8 + - - +
660A GLY 3.5 26.5 + - - +
661A GLU* 6.0 0.4 - - - -
662A MET* 4.6 19.4 + - + +
664A PHE* 3.5 23.2 - - + -
80J ILE* 3.5 30.5 - - - +
81J ASP* 5.6 4.9 - - - +
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Residues in contact with GLN 655 (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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651A GLU* 3.0 43.4 + - + +
652A GLN* 4.1 6.1 - - - +
653A GLU 3.4 0.2 - - - -
654A ARG* 1.3 83.1 - - - +
656A ALA* 1.3 58.4 + - - +
657A SER 3.3 0.4 - - - -
658A GLY* 3.4 27.4 - - - +
659A GLY* 4.6 10.3 - - - -
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Residues in contact with ALA 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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652A GLN 3.0 17.2 + - - +
653A GLU* 3.7 6.5 + - - +
654A ARG 3.3 0.6 - - - -
655A GLN* 1.3 77.3 - - - +
657A SER* 1.3 64.5 + - - +
658A GLY* 3.9 1.6 - - - -
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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