Contacts of the helix formed by residues 620 - 628 (chain N) in PDB entry 6LTJ
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 TRP 620 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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354I PRO* 3.7 25.1 - - + +
355I ILE* 5.7 4.3 - - + -
609N LEU* 6.3 0.2 - - + -
613N LEU* 4.4 14.1 - - + -
617N LYS 5.0 1.0 + - - -
618N ASP 4.9 3.7 + - - -
619N ASP* 1.3 81.5 + - - +
621N ASN* 1.3 67.2 + - - +
622N LYS 3.3 2.5 - - - -
623N VAL* 3.4 23.7 + - + +
624N SER* 3.6 13.0 + - - -
632N GLN* 4.7 4.2 - - + +
635N CYS* 4.9 8.3 - - - -
636N ILE* 3.7 49.1 - - + -
639N PHE* 4.4 14.1 - + + -
640N LEU* 4.4 4.0 - - + -
681N ALA 4.1 8.5 - - - -
682N SER* 3.8 32.7 + - - +
684N VAL 4.1 10.0 + - - -
686N PRO* 3.9 35.4 - - + +
689N ALA* 5.5 0.2 - - + -
211Q VAL* 5.8 2.2 - - + -
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Residues in contact with ASN 621 (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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354I PRO* 3.2 28.6 - - - +
619N ASP* 4.1 3.3 + - + +
620N TRP* 1.3 74.8 - - - +
622N LYS* 1.3 63.1 + - + +
624N SER* 3.9 0.6 - - - +
625N GLU* 2.8 29.7 + - - +
632N GLN* 2.4 37.0 + - - +
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Residues in contact with LYS 622 (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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612N ALA* 4.7 0.4 - - - -
616N TYR* 3.6 43.6 + - + -
619N ASP* 3.1 32.3 + - - +
620N TRP 3.3 0.6 - - - -
621N ASN* 1.3 76.9 - - + +
623N VAL* 1.3 65.5 + - - +
625N GLU* 2.7 47.6 + - + +
626N HIS* 2.9 15.4 + - - -
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Residues in contact with VAL 623 (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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609N LEU* 3.4 39.9 - - + +
612N ALA* 3.9 13.8 - - - +
613N LEU* 3.7 32.3 - - + -
616N TYR 3.8 19.7 - - - +
619N ASP* 4.1 10.8 - - - +
620N TRP* 3.4 14.3 + - + +
621N ASN 3.3 0.4 - - - -
622N LYS* 1.3 75.4 - - - +
624N SER* 1.3 59.6 + - - +
626N HIS* 2.8 19.8 + - - +
627N VAL* 2.9 16.4 + - + +
635N CYS* 4.5 7.4 - - - -
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Residues in contact with SER 624 (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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620N TRP 3.6 4.4 + - - -
621N ASN 4.7 0.2 - - - -
623N VAL* 1.3 74.9 - - - +
625N GLU* 1.3 64.4 + - - +
626N HIS 3.1 1.3 - - - -
627N VAL* 3.8 15.3 + - - -
628N GLY* 4.0 9.0 + - - -
630N ARG 4.2 0.2 + - - -
631N THR* 3.4 13.5 - - - +
632N GLN* 3.1 48.5 + - - +
635N CYS* 3.5 13.9 - - - -
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Residues in contact with GLU 625 (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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621N ASN 2.8 24.5 + - - +
622N LYS* 2.7 50.9 + - + +
624N SER* 1.3 75.4 - - - +
626N HIS* 1.3 84.6 + - - +
628N GLY* 5.2 0.9 + - - -
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Residues in contact with HIS 626 (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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608N LEU* 3.1 43.7 - - + +
611N GLU* 5.5 1.6 - - - -
612N ALA* 3.4 26.9 - - + -
615N MET* 3.9 18.9 - - + +
616N TYR* 4.8 8.2 - + - -
622N LYS* 2.9 6.6 + - - -
623N VAL 2.8 9.7 + - - +
625N GLU* 1.3 106.5 + - - +
627N VAL* 1.3 66.6 + - - +
628N GLY* 2.9 7.2 + - - -
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Residues in contact with VAL 627 (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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605N GLU* 3.2 46.1 - - - +
608N LEU* 3.8 14.7 - - - +
609N LEU* 3.6 36.8 - - + -
623N VAL 2.9 23.8 + - - +
624N SER* 3.8 7.1 + - - -
626N HIS* 1.3 70.6 - - - +
628N GLY* 1.3 53.1 + - - +
629N SER* 2.8 13.0 + - - -
630N ARG* 3.3 25.6 - - + +
635N CYS* 4.0 8.3 - - + -
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Residues in contact with GLY 628 (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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624N SER 4.0 8.9 + - - -
625N GLU 5.6 0.7 - - - -
626N HIS 2.9 7.1 + - - -
627N VAL* 1.3 75.2 - - - +
629N SER* 1.3 56.6 + - - +
630N ARG 3.8 6.1 + - - -
631N THR* 5.8 3.1 - - - +
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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