Contacts of the strand formed by residues 633 - 639 (chain N) in PDB entry 3HOU
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 VAL 633 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401N PHE* 3.8 22.7 - - + -
404N LYS 5.3 3.1 + - - +
406N LEU* 3.4 37.7 - - + +
521N LEU* 3.1 43.6 - - + +
539N LEU* 4.6 4.9 - - + -
543N SER* 4.0 12.3 - - - +
544N CYS 3.5 12.3 - - - +
545N ILE* 4.1 9.4 - - + -
631N GLY 5.5 0.4 - - - +
632N ARG* 1.3 73.3 - - - +
634N TYR* 1.3 61.3 + - - +
694N ASP* 3.9 0.9 - - - +
695N ALA* 3.6 18.5 + - - +
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Residues in contact with TYR 634 (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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41N LYS* 4.3 6.2 + - - -
521N LEU* 3.6 7.0 - - - -
543N SER* 3.4 2.3 - - - -
544N CYS* 3.0 53.2 + - + +
545N ILE* 3.3 10.5 + - - -
546N SER* 3.2 30.5 - - - -
547N VAL* 5.7 1.2 - - - +
612N GLU* 3.8 21.1 + - + +
632N ARG* 3.2 20.9 - - - -
633N VAL* 1.3 73.4 - - - +
635N ARG* 1.3 64.2 + - - +
692N TYR* 3.1 54.5 - + + +
693N ILE 3.7 4.9 - - - +
694N ASP* 3.4 27.6 - - + +
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Residues in contact with ARG 635 (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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519N TRP* 2.9 32.3 + - - +
520N GLY* 3.7 34.4 - - - +
521N LEU* 3.9 8.7 - - - +
542N MET* 4.5 2.7 - - + -
543N SER* 4.4 5.8 - - - +
634N TYR* 1.3 79.0 - - - +
636N PRO* 1.3 77.5 + - + +
637N LEU* 4.3 12.0 - - + +
692N TYR* 3.3 6.5 - - - +
693N ILE* 2.9 36.4 + - + +
698N GLU* 3.1 29.5 + - - -
703N ILE* 4.1 9.5 - - - +
742N GLU* 2.4 36.7 + - - +
748N ILE* 5.7 1.0 - - - +
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Residues in contact with PRO 636 (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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37N PHE* 4.7 3.4 - - + -
542N MET* 3.6 44.2 - - + +
635N ARG* 1.3 94.9 + - + +
637N LEU* 1.3 74.7 + - - +
681N TRP* 3.7 36.1 - - + -
690N VAL* 5.6 0.4 - - + -
691N GLU 3.3 5.4 - - - +
692N TYR* 3.9 12.8 - - + -
743N ILE* 3.5 12.3 - - + +
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Residues in contact with LEU 637 (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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635N ARG* 4.3 9.6 - - + +
636N PRO* 1.3 83.6 - - - +
638N PHE* 1.3 64.5 + - - +
639N ILE* 4.3 0.9 - - - +
690N VAL* 3.1 6.3 - - - +
691N GLU* 2.7 40.0 + - - +
693N ILE* 3.4 34.3 - - + -
703N ILE* 3.5 39.0 - - + -
740N HIS* 3.7 7.6 - - + -
741N CYS 3.0 16.8 - - - +
742N GLU* 3.3 30.1 - - + +
743N ILE* 3.7 11.4 - - + +
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Residues in contact with PHE 638 (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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25N ILE* 5.2 5.2 - - + -
30N SER* 4.6 9.2 - - - -
33N VAL* 3.6 37.5 - - + -
637N LEU* 1.3 72.7 - - - +
639N ILE* 1.3 60.8 + - - +
651N LEU* 3.4 37.2 - - + -
653N VAL* 4.0 26.5 - - + -
658N ILE* 5.9 0.7 - - + -
690N VAL* 3.2 27.4 - - + -
707N PRO* 5.3 4.5 - - + -
740N HIS* 3.0 11.4 - - - +
741N CYS* 2.8 42.9 + - + +
742N GLU 4.4 3.4 - - - -
743N ILE* 3.7 30.4 - - + +
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Residues in contact with ILE 639 (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 ARG* 3.2 50.7 - - + +
638N PHE* 1.3 75.5 - - - +
640N VAL* 1.3 58.8 + - - +
641N GLU* 3.5 20.6 - - + +
651N LEU* 3.4 4.5 - - - +
652N LYS* 2.8 41.3 + - + +
688N GLY 4.2 11.0 - - - +
689N LEU 3.2 16.3 + - - +
690N VAL 4.3 4.3 - - - +
691N GLU* 3.4 34.5 - - + +
739N THR 3.8 7.0 - - - +
740N HIS* 4.1 6.3 - - + -
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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