Contacts of the helix formed by residues 2641 - 2651 (chain D) in PDB entry 1Z5S
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 THR2641 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2640D PRO* 1.3 77.1 - - - +
2642D ALA* 1.3 78.9 + - + +
2643D GLU* 3.1 22.4 - - + +
2644D GLN* 2.6 36.3 + - + +
2645D LYS* 3.0 21.3 + - - +
2662D ASN* 4.2 5.9 + - - +
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Residues in contact with ALA2642 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2640D PRO 3.9 0.2 + - - -
2641D THR* 1.3 79.2 - - + +
2643D GLU* 1.3 61.5 + - - +
2645D LYS* 4.1 4.3 - - - +
2646D ALA* 3.1 25.0 + - - +
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Residues in contact with GLU2643 (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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2641D THR* 3.1 13.6 - - + +
2642D ALA* 1.3 77.6 - - - +
2644D GLN* 1.3 60.3 + - + +
2646D ALA* 3.7 5.9 - - + +
2647D LEU* 3.0 28.8 + - + +
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Residues in contact with GLN2644 (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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2640D PRO* 3.4 16.2 - - + +
2641D THR* 2.6 48.0 + - + +
2643D GLU* 1.3 73.9 - - + +
2645D LYS* 1.3 66.6 + - - +
2647D LEU* 2.9 18.3 + - - +
2648D ALA* 3.0 14.0 + - - +
2655D PRO 5.1 0.9 - - - -
2658D PHE* 3.2 46.6 + - + +
2659D CYS* 5.3 0.3 - - - -
2661D LYS* 4.4 10.6 - - - +
2662D ASN* 3.2 26.4 + - - +
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Residues in contact with LYS2645 (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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2639D THR* 6.2 1.3 - - + -
2640D PRO* 3.7 24.3 - - + +
2641D THR 3.0 13.4 + - - +
2642D ALA* 4.1 3.6 - - - +
2644D GLN* 1.3 78.1 - - - +
2646D ALA* 1.3 54.0 + - - +
2648D ALA* 3.4 4.0 + - - +
2649D THR* 2.6 43.2 + - - +
2655D PRO* 4.4 26.0 - - + +
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Residues in contact with ALA2646 (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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2642D ALA 3.1 17.2 + - - +
2643D GLU* 3.7 7.2 - - - +
2644D GLN 3.1 0.6 - - - -
2645D LYS* 1.3 78.6 - - - +
2647D LEU* 1.3 64.2 + - - +
2649D THR* 3.5 10.0 - - - -
2650D LYS* 3.2 18.9 + - - +
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Residues in contact with LEU2647 (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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11A GLN* 4.6 11.4 - - - +
2643D GLU* 3.0 14.8 + - + +
2644D GLN* 2.9 10.6 + - - +
2646D ALA* 1.3 73.9 - - - +
2648D ALA* 1.3 59.0 + - - +
2650D LYS* 2.8 29.9 + - + +
2651D LEU* 3.0 29.7 + - + +
2658D PHE* 3.0 42.0 - - + -
2661D LYS* 5.3 6.5 - - - +
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Residues in contact with ALA2648 (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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2644D GLN 3.0 4.8 + - - +
2645D LYS* 3.6 7.2 - - - +
2647D LEU* 1.3 80.0 - - - +
2649D THR* 1.3 52.5 + - - +
2651D LEU* 3.0 3.3 + - - +
2652D LYS 2.8 31.0 + - - -
2653D LEU* 2.9 37.1 + - + +
2654D PRO 4.3 2.5 - - - +
2655D PRO* 4.3 17.3 - - + +
2657D PHE* 4.8 0.4 - - + -
2658D PHE* 3.6 22.4 - - + -
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Residues in contact with THR2649 (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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2645D LYS* 2.6 35.8 + - - +
2646D ALA* 3.5 11.5 - - - +
2647D LEU 3.1 0.2 - - - -
2648D ALA* 1.3 77.2 - - - +
2650D LYS* 1.3 63.1 + - - +
2652D LYS* 3.6 15.3 + - - +
2653D LEU 5.2 1.1 - - - -
2655D PRO* 5.6 4.4 - - - +
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Residues in contact with LYS2650 (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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4A ILE* 3.3 38.6 - - + +
2646D ALA 3.2 9.2 + - - +
2647D LEU* 2.8 17.6 + - + +
2649D THR* 1.3 82.8 - - - +
2651D LEU* 1.3 62.9 + - + +
2652D LYS* 3.3 12.1 + - - +
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Residues in contact with LEU2651 (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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4A ILE* 3.4 33.7 - - + -
7A SER* 4.4 4.3 - - - -
8A ARG* 2.4 53.7 + - + +
11A GLN* 3.5 31.6 - - + -
69A PRO* 5.0 0.4 - - - +
2647D LEU* 3.0 31.5 + - + +
2648D ALA 3.0 1.5 + - - +
2650D LYS* 1.3 87.0 - - + +
2652D LYS* 1.3 60.0 + - - +
2653D LEU* 3.0 26.2 - - + -
2658D PHE* 4.3 0.7 - - + -
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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