Contacts of the strand formed by residues 690 - 694 (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 690 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33N VAL* 5.0 0.9 - - + -
605N ARG* 6.2 0.2 - - - -
637N LEU 3.1 12.6 - - - +
638N PHE* 3.2 41.7 - - + -
639N ILE* 4.2 3.1 - - - +
653N VAL* 4.4 4.0 - - + -
681N TRP* 4.0 33.7 - - + -
684N LEU* 3.6 29.4 - - + +
685N LEU* 3.5 27.1 - - + +
688N GLY* 4.7 0.7 - - - -
689N LEU* 1.3 77.8 + - + +
691N GLU* 1.3 63.7 + - - +
692N TYR* 6.0 0.2 - - - -
743N ILE* 4.8 2.2 - - + -
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Residues in contact with GLU 691 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601N ARG* 4.3 5.8 - - - +
604N ARG* 2.4 48.7 + - - +
605N ARG* 3.6 29.0 + - + +
611N PRO* 6.3 0.2 - - + -
636N PRO* 3.3 0.8 - - - +
637N LEU* 2.7 40.6 + - - +
639N ILE* 3.4 18.3 - - + +
685N LEU* 4.6 4.7 - - + -
690N VAL* 1.3 77.3 - - - +
692N TYR* 1.3 70.0 + - - +
693N ILE* 3.4 9.3 + - + +
697N GLU* 5.4 0.7 - - - -
740N HIS* 3.2 26.3 + - + +
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Residues in contact with TYR 692 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37N PHE* 5.2 3.4 - + - -
40N GLU* 5.6 0.2 + - - -
41N LYS* 3.7 26.9 + - + +
544N CYS* 5.4 1.6 - - - -
604N ARG* 4.6 10.7 + - - -
611N PRO* 3.1 35.8 + - + +
612N GLU* 4.2 12.8 - - + +
614N SER* 5.4 0.5 - - - -
634N TYR* 3.1 47.6 - + + +
635N ARG 3.3 4.5 - - - -
636N PRO* 3.9 13.7 - - + -
681N TRP* 3.1 44.8 + + - -
685N LEU* 4.4 21.4 - - + +
691N GLU* 1.3 77.5 - - - +
693N ILE* 1.3 62.1 + - - +
694N ASP 3.6 3.3 + - - -
697N GLU* 5.1 1.4 - - - +
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Residues in contact with ILE 693 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
521N LEU* 5.2 0.2 - - - +
634N TYR* 3.9 2.0 - - - -
635N ARG* 2.9 35.7 + - + +
637N LEU* 3.4 42.0 - - + +
691N GLU* 4.0 12.8 - - + +
692N TYR* 1.3 69.1 - - - +
694N ASP* 1.3 77.1 + - - +
697N GLU* 4.2 12.1 - - + -
698N GLU* 3.6 29.9 - - + +
701N ILE* 3.5 19.7 - - + -
703N ILE* 4.9 0.2 - - + -
740N HIS* 3.6 20.9 - - + +
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Residues in contact with ASP 694 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
402N GLY* 5.1 2.9 - - - +
521N LEU* 5.4 1.3 - - - -
612N GLU 5.5 0.9 - - - +
614N SER* 3.2 30.1 + - - -
627N PHE* 5.4 0.9 - - - +
632N ARG* 3.3 38.1 + - + +
633N VAL 4.1 4.5 - - - +
634N TYR* 3.4 21.7 - - + +
692N TYR 3.6 5.8 + - - +
693N ILE* 1.3 89.6 - - - +
695N ALA* 1.3 65.3 + - - +
696N GLU* 3.7 13.2 + - - +
697N GLU* 3.1 22.3 + - - +
698N GLU* 3.3 8.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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