Contacts of the helix formed by residues 699 - 704 (chain B) in PDB entry 5IYB
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 HIS 699 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLN 5.6 0.4 - - - -
24B GLU* 5.9 1.0 + - - -
26B CYS* 4.2 14.4 - - - -
27B TRP* 3.6 26.7 + + - -
30B ILE* 3.7 15.3 - - + -
529B MET* 5.4 0.5 - - - +
697B GLU* 3.2 13.4 - - - +
698B ILE* 1.3 84.0 + - - +
700B PRO* 1.3 88.7 - - + +
701B SER* 3.1 35.1 + - - -
702B MET* 3.5 21.2 - - + +
703B ILE* 5.5 0.2 - - - +
1000B THR* 4.0 17.4 - - + +
1002B PHE* 4.0 18.6 + - + -
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Residues in contact with PRO 700 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PRO* 3.6 30.2 - - + +
506B TRP* 5.5 1.3 - - + -
677B MET* 3.8 33.7 - - + +
678B THR* 4.7 9.6 - - + -
697B GLU* 4.4 9.2 - - + +
699B HIS* 1.3 94.6 - - + +
701B SER* 1.3 60.9 + - - +
702B MET 3.0 7.2 + - - -
703B ILE* 3.2 27.1 + - + +
1002B PHE* 3.6 15.8 - - + +
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Residues in contact with SER 701 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TRP* 4.1 3.8 - - - -
699B HIS* 3.1 25.2 + - - -
700B PRO* 1.3 76.3 - - - +
702B MET* 1.3 75.3 + - - +
703B ILE* 3.1 2.2 - - - -
704B LEU* 3.1 31.8 + - - +
709B SER* 5.3 0.5 + - - -
763B SER* 4.0 7.6 + - - -
1000B THR* 4.9 0.5 - - - +
1001B PRO* 3.5 31.4 - - - -
1002B PHE* 3.5 12.3 - - - -
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Residues in contact with MET 702 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B TRP* 4.3 12.8 - - + -
30B ILE* 4.4 23.8 - - + -
34B PHE* 4.5 8.7 - - + -
527B ALA* 3.4 15.8 - - - +
528B LEU* 3.7 29.4 + - + -
529B MET* 4.0 32.4 - - + +
698B ILE* 5.0 6.7 - - + -
699B HIS* 3.5 28.7 - - + +
700B PRO 3.0 1.4 - - - -
701B SER* 1.3 93.3 - - - +
703B ILE* 1.3 59.6 + - - +
704B LEU 2.9 8.9 + - - -
709B SER* 5.9 0.2 - - - +
763B SER* 3.3 30.7 - - - +
766B TYR* 5.7 0.7 - - + -
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Residues in contact with ILE 703 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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833A PRO* 6.0 0.9 - - + +
836A PHE* 4.0 24.0 - - + -
837A PHE* 4.5 10.7 - - + -
506B TRP* 3.7 47.6 - - + +
507B GLY* 4.2 19.9 + - - +
509B VAL 4.4 2.6 - - - +
510B CYS* 4.1 1.6 - - - -
511B PRO* 3.3 40.8 - - + +
527B ALA* 3.6 13.0 - - - +
529B MET* 5.8 0.2 - - - -
623B ARG* 4.8 2.7 - - - +
697B GLU* 4.6 6.7 - - - +
699B HIS 5.5 0.2 - - - +
700B PRO 3.2 19.7 - - - +
701B SER* 4.6 1.6 - - - -
702B MET* 1.3 77.2 - - - +
704B LEU* 1.3 62.1 + - + +
1002B PHE* 5.1 5.2 - - + -
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Residues in contact with LEU 704 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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836A PHE* 4.2 13.5 - - + -
511B PRO* 3.9 22.4 - - + -
512B ALA* 5.5 0.9 - - + +
527B ALA* 3.9 3.6 - - - -
528B LEU* 3.2 24.6 + - - +
701B SER* 3.1 19.6 + - - +
702B MET* 2.9 3.6 - - - +
703B ILE* 1.3 87.0 - - + +
705B GLY* 1.3 60.5 + - - +
708B ALA* 3.3 41.5 - - + +
709B SER* 3.4 13.3 + - - +
714B PRO* 4.3 18.6 - - + -
1001B PRO* 4.7 11.9 - - + -
1002B PHE* 5.8 2.0 - - + -
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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
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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