Contacts of the helix formed by residues 744 - 749 (chain B) in PDB entry 1Y1V
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 744 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27B ALA* 6.3 3.1 - - + +
30B SER* 4.4 11.7 + - - +
31B TRP* 3.8 28.2 + + + -
34B ILE* 4.1 16.6 - - + -
742B GLU* 3.3 11.5 - - - +
743B ILE* 1.3 81.4 + - - +
745B PRO* 1.3 81.6 - - + +
746B SER* 2.9 47.1 - - - +
747B MET* 3.4 17.7 + - - +
1045B SER* 5.8 1.2 - - - -
1046B PRO* 5.5 2.2 - - - +
1047B PHE* 3.7 24.1 + - - -
1048B THR* 5.2 5.6 - - + +
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Residues in contact with PRO 745 (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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810A PRO* 3.7 24.9 - - + -
519B TRP* 5.3 2.7 - - + -
705B MET* 4.5 20.0 - - + +
706B GLN* 6.0 4.9 - - + -
742B GLU* 4.5 10.2 - - + -
744B HIS* 1.3 98.4 - - + +
746B SER* 1.3 54.2 + - - +
747B MET 2.6 18.6 + - - -
748B ILE* 2.6 32.3 + - + +
1047B PHE* 3.4 31.0 - - + +
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Residues in contact with SER 746 (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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31B TRP* 3.4 10.3 - - - -
541B LEU* 5.6 1.0 - - - +
744B HIS* 2.9 30.2 - - - -
745B PRO* 1.3 77.2 - - - +
747B MET* 1.3 75.0 + - - +
748B ILE* 2.8 8.4 + - - -
749B LEU* 3.0 27.1 + - - +
806B THR* 5.8 0.2 - - - -
808B ALA* 5.4 6.7 - - - +
1046B PRO* 4.2 24.5 - - - -
1047B PHE* 3.7 13.1 - - - -
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Residues in contact with MET 747 (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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31B TRP* 4.2 6.7 - - - -
34B ILE* 3.9 20.9 - - + -
38B PHE* 3.8 13.2 - - + -
520B GLY* 4.1 3.2 - - - +
540B SER* 3.1 23.4 - - - -
541B LEU* 3.2 52.7 + - + -
542B MET* 3.2 48.7 + - + +
743B ILE* 5.3 1.1 - - + -
744B HIS 3.4 18.2 - - - +
745B PRO 2.6 5.3 + - - -
746B SER* 1.3 84.8 - - - +
748B ILE* 1.3 54.8 + - - -
749B LEU 3.1 6.0 + - - +
808B ALA* 5.5 3.4 - - - -
811B TYR* 6.1 0.7 - - + -
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Residues in contact with ILE 748 (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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810A PRO 4.8 0.7 - - - +
813A PHE* 4.2 17.7 - - + -
814A PHE* 4.9 4.3 - - + -
519B TRP* 3.5 46.2 - - + +
520B GLY* 3.3 31.2 - - - +
522B VAL 3.2 4.0 - - - +
523B CYS* 3.5 1.0 - - - -
524B PRO* 3.0 24.6 - - + +
540B SER* 3.1 16.4 + - - -
742B GLU* 6.2 0.4 - - - -
745B PRO* 2.6 26.5 + - + +
746B SER 2.8 2.9 + - - +
747B MET* 1.3 71.7 - - - +
749B LEU* 1.3 61.7 + - + +
1047B PHE* 3.7 28.3 - - + -
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Residues in contact with LEU 749 (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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813A PHE* 3.8 31.0 - - + -
523B CYS* 3.9 3.8 - - - -
524B PRO* 3.8 14.6 - - + -
525B ALA* 5.6 0.4 - - + +
540B SER* 2.9 22.4 - - - -
541B LEU* 3.2 11.6 + - + +
746B SER* 3.0 18.9 + - - +
747B MET 3.7 0.5 - - - +
748B ILE* 1.3 86.5 - - + +
750B GLY* 1.3 60.2 + - - +
753B ALA* 4.1 25.1 - - + -
754B SER* 4.1 21.1 - - - +
759B PRO* 4.5 10.1 - - + -
1046B PRO* 4.1 26.0 - - + -
1047B PHE* 5.6 1.8 - - + -
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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