Contacts of the helix formed by residues 683 - 693 (chain C) in PDB entry 3T6A
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 683 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638C LYS* 5.9 4.0 - - - +
679C LEU* 2.8 38.1 + - + +
682C LYS* 1.3 94.3 + - + +
684C LEU* 1.3 77.3 + - + +
685C LYS 3.5 0.4 - - - -
686C PRO* 3.3 3.3 - - - +
687C PHE* 3.1 25.6 + - - +
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Residues in contact with LEU 684 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631C ILE* 4.1 16.8 - - + -
634C ALA* 4.1 21.8 - - + -
635C VAL* 4.0 23.3 - - + -
638C LYS* 4.5 18.4 - - + +
647C PHE* 4.0 16.8 - - + -
651C MET* 3.5 19.1 - - + +
679C LEU* 3.0 16.1 + - + +
680C TYR* 3.3 17.0 - - + +
683C GLN* 1.3 92.9 - - + +
685C LYS* 1.3 57.9 + - - +
687C PHE* 3.3 5.6 + - - +
688C SER* 2.8 29.6 + - - -
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Residues in contact with LYS 685 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651C MET* 3.9 9.4 - - + -
655C GLU* 5.0 12.8 - - - +
680C TYR* 3.0 49.8 + - + +
681C GLU* 3.2 40.1 + - - +
684C LEU* 1.3 73.4 - - - +
686C PRO* 1.3 73.7 - - + +
688C SER* 3.1 5.7 + - - -
689C LYS* 2.9 22.0 + - - +
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Residues in contact with PRO 686 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681C GLU 3.6 11.9 - - - +
682C LYS* 3.3 20.2 - - - +
683C GLN 3.3 15.3 - - - +
685C LYS* 1.3 95.0 - - + +
687C PHE* 1.3 58.7 + - - +
689C LYS* 3.2 10.6 + - + +
690C LEU* 3.1 28.0 + - + +
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Residues in contact with PHE 687 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638C LYS* 3.4 43.3 - - + -
644C LEU* 4.3 7.9 - - + -
647C PHE* 3.7 22.2 - + - -
683C GLN 3.1 18.4 + - - +
684C LEU 3.5 2.2 - - - +
686C PRO* 1.3 78.1 - - - +
688C SER* 1.3 60.6 + - - +
690C LEU* 3.2 14.3 + - + +
691C LEU* 3.0 50.8 + - + +
699C CYS* 3.5 39.9 - - + -
701C PRO* 4.1 18.6 - - + -
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Residues in contact with SER 688 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647C PHE* 4.4 14.4 - - - -
648C SER* 5.8 2.4 - - - -
651C MET* 4.1 22.8 - - - +
655C GLU* 4.2 12.8 + - - -
684C LEU 2.8 17.0 + - - -
685C LYS* 3.3 10.5 - - - -
687C PHE* 1.3 74.3 - - - +
689C LYS* 1.3 61.8 + - - +
691C LEU* 3.4 8.5 + - - +
692C HIS* 3.1 22.7 + - - +
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Residues in contact with LYS 689 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685C LYS 2.9 12.9 + - - +
686C PRO* 3.5 12.1 - - + +
687C PHE 3.2 0.2 - - - -
688C SER* 1.3 74.3 - - - +
690C LEU* 1.3 66.1 + - + +
692C HIS* 3.0 17.2 + - + +
693C GLU* 2.6 49.9 + - + +
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Residues in contact with LEU 690 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686C PRO* 3.1 19.1 + - + +
687C PHE* 3.4 15.0 - - + +
689C LYS* 1.3 76.1 - - + +
691C LEU* 1.3 63.4 + - - +
693C GLU* 3.2 19.1 + - - +
695C ARG* 3.1 54.3 + - + +
699C CYS* 4.3 28.5 - - + -
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Residues in contact with LEU 691 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644C LEU* 4.4 15.5 - - + -
647C PHE* 4.2 17.7 - - + -
648C SER* 5.5 0.7 - - - -
687C PHE* 3.0 57.7 + - + +
688C SER* 3.6 7.6 - - - +
689C LYS 3.2 0.2 - - - -
690C LEU* 1.3 75.8 - - - +
692C HIS* 1.3 58.7 + - - +
694C GLY* 2.9 20.1 + - - -
695C ARG 4.5 2.9 - - - +
696C GLU* 3.6 33.5 + - + +
699C CYS* 4.4 4.0 - - - +
709C LEU* 3.4 41.5 - - + +
743C HIS* 3.5 1.2 - - - -
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Residues in contact with HIS 692 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688C SER 3.1 12.9 + - - +
689C LYS* 3.0 12.6 + - + +
691C LEU* 1.3 76.9 - - - +
693C GLU* 1.3 58.7 + - + +
694C GLY 3.1 0.4 - - - -
709C LEU* 4.7 4.9 - - - -
712C PRO* 4.2 12.1 - - + +
728C ASP* 3.8 32.1 + - - -
730C TRP* 5.5 6.6 - + - -
734C ASP* 3.3 39.9 + - + +
739C ILE* 3.8 9.8 - - + +
743C HIS* 3.0 17.5 + - - -
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Residues in contact with GLU 693 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689C LYS* 2.6 52.2 + - + +
690C LEU* 3.6 23.8 - - - +
691C LEU 3.1 0.6 - - - -
692C HIS* 1.3 80.7 - - + +
694C GLY* 1.3 58.2 + - - +
695C ARG* 3.4 13.4 + - + +
739C ILE* 4.1 30.0 - - + +
742C ASN* 2.9 26.6 + - - +
743C HIS* 3.8 2.5 - - - -
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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