Contacts of the strand formed by residues 442 - 447 (chain A) in PDB entry 5N4D
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 PHE 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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397A LEU* 4.0 26.2 - - + -
398A ALA* 3.9 34.3 - - + -
418A LEU* 4.0 18.6 - - + -
420A LEU* 5.4 0.4 - - + -
430A ALA* 3.5 31.2 - - + -
431A ARG 3.4 11.4 - - - -
432A TYR* 4.4 14.8 - + + -
439A THR 5.4 1.3 + - - +
440A GLN* 3.4 4.8 - - - -
441A ARG* 1.3 77.4 - - - +
443A SER* 1.3 64.3 + - - +
444A ILE* 4.5 14.1 - - + -
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Residues in contact with SER 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A ALA* 3.3 7.5 - - - +
431A ARG* 2.8 64.1 + - - +
440A GLN 5.6 2.5 - - - -
441A ARG 4.0 1.4 + - - -
442A PHE* 1.3 79.9 - - - +
444A ILE* 1.3 70.4 + - - +
445A LEU* 5.3 0.2 - - - -
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Residues in contact with ILE 444 (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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420A LEU* 5.6 2.0 - - + -
428A THR* 3.7 22.7 - - + -
429A ILE 3.8 6.5 - - - +
430A ALA* 3.9 16.4 - - + -
442A PHE* 4.5 11.0 - - + -
443A SER* 1.3 80.7 + - - +
445A LEU* 1.3 63.2 + - - +
446A ARG* 3.8 9.9 - - - +
447A THR* 3.7 22.9 - - - +
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Residues in contact with LEU 445 (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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87A PRO* 3.5 37.9 - - + -
117A LEU* 4.0 27.1 - - + -
118A PRO 4.6 2.9 - - - +
120A PHE* 3.8 28.7 + - + +
121A SER 5.9 0.2 + - - -
417A PHE* 3.8 10.1 - - + -
429A ILE* 2.8 26.9 + - + +
431A ARG* 4.5 15.5 - - + +
443A SER* 3.8 3.6 + - - -
444A ILE* 1.3 76.0 - - - +
446A ARG* 1.4 71.2 + - + +
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Residues in contact with ARG 446 (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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84A PHE* 3.3 60.3 - - + +
85A SER 4.9 3.1 + - - -
97A TRP* 4.0 3.4 - - - +
120A PHE* 3.4 51.3 + - + +
123A GLY* 5.7 0.2 - - - -
124A ASP* 2.8 42.8 + - - -
427A GLY 4.1 0.5 - - - +
428A THR* 3.5 2.3 - - - -
429A ILE* 2.9 38.9 + - + +
444A ILE* 3.7 4.0 - - - +
445A LEU* 1.4 98.8 - - + +
447A THR* 1.3 63.5 + - - +
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Residues in contact with THR 447 (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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84A PHE* 3.7 10.3 - - - -
426A PRO* 5.9 4.0 - - + -
427A GLY 3.7 3.6 - - - +
428A THR* 4.1 16.1 + - - +
444A ILE* 3.7 15.6 - - - +
446A ARG* 1.3 74.6 + - - +
448A THR* 1.3 75.0 + - - +
449A LYS* 3.4 31.4 + - + +
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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