Contacts of the helix formed by residues 683 - 693 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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638D LYS* 5.3 5.1 - - - +
678D ILE* 4.8 1.3 - - + +
679D LEU* 3.1 41.4 + - + +
682D LYS* 1.3 90.0 + - + +
684D LEU* 1.3 70.9 + - + +
685D LYS 3.5 0.6 + - - -
686D PRO* 3.7 3.3 - - - +
687D PHE* 3.3 23.4 + - - +
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Residues in contact with LEU 684 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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631D ILE* 4.0 23.8 - - + +
634D ALA* 4.4 5.4 - - + -
635D VAL* 4.0 33.7 - - + +
638D LYS* 4.2 23.3 - - + +
639D ASP* 6.0 0.9 - - - +
647D PHE* 3.7 23.2 - - + -
651D MET* 4.0 18.8 - - + +
679D LEU* 3.0 9.9 + - + +
680D TYR* 3.4 17.0 - - + +
683D GLN* 1.3 85.1 - - + +
685D LYS* 1.3 65.7 + - - +
687D PHE* 3.2 6.5 + - - +
688D SER* 2.9 23.6 + - - -
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Residues in contact with LYS 685 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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651D MET* 4.1 10.3 - - + +
655D GLU* 5.3 10.1 - - - +
680D TYR* 2.9 47.8 + - + +
681D GLU* 2.8 46.9 + - - +
684D LEU* 1.3 73.6 - - - +
686D PRO* 1.3 70.9 - - + +
688D SER* 3.3 6.6 + - - -
689D LYS* 3.2 19.4 + - - +
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Residues in contact with PRO 686 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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681D GLU 3.3 14.6 - - - +
682D LYS* 3.7 17.9 - - - +
683D GLN 3.7 9.6 - - - +
685D LYS* 1.3 97.3 - - + +
687D PHE* 1.3 56.2 + - - +
689D LYS* 3.2 15.1 + - + +
690D LEU* 3.0 31.7 + - - +
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Residues in contact with PHE 687 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D LYS* 3.5 49.8 - - + -
644D LEU* 3.9 18.4 - - + -
647D PHE* 3.6 16.2 - + - -
683D GLN 3.3 17.3 + - - +
684D LEU* 3.2 5.9 + - - +
686D PRO* 1.3 77.6 - - - +
688D SER* 1.3 57.4 + - - +
690D LEU* 3.1 12.3 + - + +
691D LEU* 2.9 60.1 + - + +
699D CYS* 3.5 38.8 - - + -
701D PRO* 4.2 8.3 - - + -
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Residues in contact with SER 688 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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647D PHE* 4.3 12.8 - - - -
648D SER* 5.4 4.9 - - - -
651D MET* 3.9 31.8 - - - +
655D GLU* 4.2 9.6 + - - -
684D LEU 2.9 12.6 + - - -
685D LYS* 3.4 10.5 - - - -
687D PHE* 1.3 76.6 - - - +
689D LYS* 1.3 56.7 + - - +
691D LEU* 3.5 6.5 + - - +
692D HIS* 3.1 28.6 + - - +
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Residues in contact with LYS 689 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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685D LYS 3.2 11.4 + - - +
686D PRO* 3.2 16.8 + - + +
687D PHE 3.1 0.4 - - - -
688D SER* 1.3 75.8 - - - +
690D LEU* 1.3 66.6 + - + +
692D HIS* 3.4 6.6 + - - +
693D GLU* 3.1 48.0 + - + +
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Residues in contact with LEU 690 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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686D PRO 3.0 15.6 + - - +
687D PHE* 3.1 14.6 + - + +
689D LYS* 1.3 76.4 - - + +
691D LEU* 1.3 66.5 + - - +
693D GLU* 3.2 21.0 + - - +
695D ARG* 3.0 50.6 + - + +
698D THR* 6.4 0.4 - - + -
699D CYS* 4.4 27.6 - - + -
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Residues in contact with LEU 691 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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644D LEU* 4.1 21.8 - - + -
647D PHE* 4.0 19.1 - - + -
648D SER* 5.7 0.9 - - - -
687D PHE* 2.9 59.4 + - + +
688D SER* 3.6 7.6 - - - +
690D LEU* 1.3 75.3 - - - +
692D HIS* 1.3 59.1 + - - +
694D GLY* 2.9 21.5 + - - -
695D ARG 4.0 0.2 + - - -
696D GLU* 3.7 34.9 + - + +
699D CYS* 4.4 3.1 - - - -
709D LEU* 3.5 33.4 - - + +
743D HIS* 3.5 1.2 - - - -
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Residues in contact with HIS 692 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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688D SER 3.1 18.2 + - - +
689D LYS* 3.4 7.4 + - - +
690D LEU 3.2 0.4 - - - -
691D LEU* 1.3 76.7 - - - +
693D GLU* 1.3 59.6 + - + +
694D GLY 3.1 0.7 - - - -
709D LEU* 4.5 5.6 - - + -
712D PRO* 4.2 19.5 - - + +
728D ASP* 4.2 19.8 + - - -
730D TRP* 5.6 1.9 - + - -
734D ASP* 3.3 38.7 + - - -
739D ILE* 3.8 9.3 - - + +
743D HIS* 3.0 17.6 + - - -
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Residues in contact with GLU 693 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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689D LYS* 3.1 53.8 + - + +
690D LEU* 3.6 21.7 - - - +
691D LEU 3.1 0.4 - - - -
692D HIS* 1.3 81.1 - - - +
694D GLY* 1.3 55.9 + - - +
695D ARG* 3.4 15.2 + - + +
739D ILE* 3.9 30.6 - - + +
742D ASN* 3.0 25.8 + - - +
743D HIS* 3.9 2.0 - - - -
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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