Contacts of the strand formed by residues 566 - 571 (chain G) in PDB entry 1H1V
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 ALA 566 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541G VAL* 2.7 38.2 + - - +
565G ASP* 1.3 73.9 - - - +
567G PHE* 1.3 59.4 + - - +
577G LEU* 4.9 1.6 - - + -
578G TRP 3.5 9.9 - - - +
579G VAL* 4.3 7.6 - - + +
583G ALA* 4.4 7.9 - - + -
587G GLU* 3.6 34.2 + - + +
588G LYS* 4.6 2.9 - - - +
591G ALA* 4.1 9.6 - - + -
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Residues in contact with PHE 567 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538G LEU* 3.5 28.3 - - + -
539G PHE 3.0 15.0 - - - -
540G GLN* 3.3 35.2 - - + -
541G VAL* 4.7 0.7 - - - -
554G VAL* 5.6 1.6 - - + -
560G ALA* 3.2 23.3 - - + -
561G LEU* 3.6 9.4 - - + -
562G ASN* 3.3 33.7 - - + -
565G ASP* 3.8 15.5 - - + -
566G ALA* 1.3 81.7 - - - +
568G VAL* 1.3 67.0 + - - +
577G LEU* 3.5 5.4 - - - +
578G TRP* 2.8 54.5 + + + +
591G ALA* 5.5 0.2 - - - -
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Residues in contact with VAL 568 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537G ARG 3.8 0.2 - - - +
538G LEU* 3.0 7.6 - - - +
539G PHE* 2.9 35.7 + - + +
541G VAL* 4.8 2.9 - - + +
567G PHE* 1.3 80.2 - - - +
569G LEU* 1.3 62.6 + - - +
570G LYS* 4.4 9.6 - - + +
576G TYR 3.6 3.1 - - - +
577G LEU* 4.2 5.4 - - + -
591G ALA* 3.3 34.1 - - + +
594G LEU* 3.3 28.9 - - + -
595G LEU* 3.5 33.4 - - + -
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Residues in contact with LEU 569 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536G THR* 4.4 4.9 - - - +
537G ARG 3.4 14.6 - - - +
538G LEU* 4.4 9.9 - - + -
556G PRO* 5.1 2.5 - - + -
567G PHE 4.3 0.4 - - - -
568G VAL* 1.3 72.9 - - - +
570G LYS* 1.3 67.2 + - - +
571G THR* 4.3 6.7 - - + -
575G ALA* 3.0 5.9 - - - -
576G TYR* 2.8 43.0 + - + +
578G TRP* 5.6 1.1 - - + +
614G PHE* 3.9 27.4 - - + +
617G ALA* 3.6 32.1 - - + -
618G LEU* 3.3 37.7 - - + -
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Residues in contact with LYS 570 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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536G THR* 3.3 2.1 + - - -
537G ARG* 2.8 49.8 + - + +
539G PHE* 5.7 3.3 - - + -
568G VAL* 3.9 10.6 + - + +
569G LEU* 1.3 72.5 - - - +
571G THR* 1.3 60.3 + - - +
572G PRO* 3.5 24.7 - - + -
574G ALA 5.6 0.2 - - - +
575G ALA* 3.8 9.0 - - + -
595G LEU* 5.7 3.8 - - + -
598G LEU* 3.2 23.5 + - + +
599G ARG* 2.7 34.0 + - - +
600G ALA* 4.3 9.0 - - + -
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Residues in contact with THR 571 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535G SER 4.8 1.5 + - - -
536G THR* 3.0 29.5 + - - -
569G LEU* 4.3 6.3 - - - +
570G LYS* 1.3 73.4 - - - +
572G PRO* 1.3 55.8 - - - +
573G SER* 2.3 32.3 + - - -
574G ALA* 2.4 49.7 + - + +
575G ALA* 3.5 5.8 - - - +
576G TYR* 4.5 1.8 - - + -
617G ALA* 4.1 22.6 - - + +
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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
------------------------------------------------------------
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