Contacts of the strand formed by residues 604 - 608 (chain A) in PDB entry 1H5P
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 GLU 604 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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602A GLN* 2.8 23.2 + - + +
603A SER* 1.3 88.0 - - - +
605A LEU* 1.3 63.6 + - - +
606A PRO* 3.9 6.2 - - - +
615A THR* 3.2 29.4 - - + +
616A LEU 3.2 7.4 - - - +
617A TYR* 3.9 29.1 + - + -
618A LYS* 3.4 4.7 + - - +
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Residues in contact with LEU 605 (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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598A ILE* 3.4 25.8 - - + +
599A ASN 3.3 27.1 - - - +
600A PHE* 3.4 20.2 - - + +
604A GLU* 1.3 72.5 - - - +
606A PRO* 1.3 66.4 - - + +
607A VAL 3.4 0.2 + - - -
615A THR* 5.0 1.6 - - - -
616A LEU* 2.9 52.6 + - + +
618A LYS* 3.2 21.9 - - - +
621A PHE* 4.9 7.2 - - + -
661A CYS* 3.4 25.6 - - - -
669A LEU* 4.2 13.7 - - + -
674A PHE* 5.4 4.5 - - + -
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Residues in contact with PRO 606 (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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598A ILE* 4.3 9.0 - - + -
599A ASN 5.8 0.2 - - - +
604A GLU 3.9 6.3 - - - +
605A LEU* 1.3 93.8 - - + +
607A VAL* 1.3 60.0 + - - +
608A THR* 5.8 0.2 - - - -
613A LYS* 5.2 15.0 - - + +
614A GLY 3.8 6.5 - - - +
615A THR* 5.2 2.2 - - + -
661A CYS* 3.2 7.8 - - - -
662A GLY* 2.9 41.8 + - - +
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Residues in contact with VAL 607 (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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606A PRO* 1.3 72.8 - - - +
608A THR* 1.3 63.0 + - - +
609A CYS 4.3 0.7 - - - -
612A VAL 4.7 0.2 - - - -
613A LYS* 3.1 9.5 - - - +
614A GLY* 2.8 50.2 + - - +
615A THR 4.0 0.7 - - - +
616A LEU* 4.0 24.5 - - + +
630A ILE* 3.7 29.6 - - + -
643A PHE* 4.7 1.6 - - + -
659A ILE* 4.4 12.8 - - + -
660A ARG 3.2 13.9 - - - +
661A CYS* 3.5 23.8 - - + +
666A LEU* 5.1 4.5 - - + -
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Residues in contact with THR 608 (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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606A PRO 5.8 0.4 - - - -
607A VAL* 1.3 83.3 - - - +
609A CYS* 1.3 61.3 + - - +
610A GLY 3.7 1.7 + - - -
611A GLU* 5.2 8.7 - - - -
612A VAL 3.9 4.0 - - - -
613A LYS* 3.4 35.2 - - + +
659A ILE* 4.1 0.4 - - - -
660A ARG* 2.8 60.6 + - - +
661A CYS 4.4 0.5 + - - -
662A GLY 4.7 5.0 + - - -
663A GLY 5.5 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