Contacts of the helix formed by residues 1109 - 1116 (chain B) in PDB entry 5YWB
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 PRO1109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510B LYS* 4.9 2.5 - - - -
1108B ALA* 1.3 89.8 - - + +
1110B MET* 1.3 66.8 + - - +
1111B ARG* 3.2 8.5 - - + +
1112B PHE* 3.0 25.9 + - + +
1113B PHE* 3.3 11.8 + - - -
1322B GLU* 4.1 14.6 - - + -
1323B ALA* 4.1 6.5 - - + +
1325B SER* 3.4 27.1 - - - +
1397B ASP* 5.7 9.9 - - + +
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Residues in contact with MET1110 (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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506B MET 4.2 5.4 - - - +
507B LYS* 3.6 53.8 - - + +
510B LYS* 4.6 6.8 - - + +
1108B ALA 4.0 0.4 + - - -
1109B PRO* 1.3 73.2 - - - +
1111B ARG* 1.3 63.2 + - - +
1113B PHE* 3.2 21.7 + - + +
1114B GLU* 2.9 34.9 + - + +
1395B MET* 3.6 48.2 + - + +
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Residues in contact with ARG1111 (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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1109B PRO* 3.2 8.6 - - + +
1110B MET* 1.3 78.6 - - - +
1112B PHE* 1.3 54.7 + - - +
1114B GLU* 4.0 13.6 + - - +
1115B THR* 2.7 54.2 + - - +
1354B TYR* 3.6 24.6 - - - +
1355B ASP* 3.6 40.8 + - - +
1358B LEU* 5.1 3.8 - - - +
1395B MET 5.3 2.6 + - - +
1397B ASP* 4.7 15.9 - - - +
2502B ADP 3.3 36.3 + - - -
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Residues in contact with PHE1112 (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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1105B ILE* 4.5 20.2 - - + -
1108B ALA* 3.6 25.8 - - + -
1109B PRO* 3.0 23.8 + - + +
1111B ARG* 1.3 81.5 - - - +
1113B PHE* 1.3 68.5 + + - +
1115B THR* 4.4 4.9 - - + -
1116B THR* 2.8 59.3 + - + -
1121B ILE* 4.8 11.4 - - + -
1318B LEU* 5.4 6.7 - - + -
1321B THR* 3.6 37.0 - - + -
1322B GLU* 4.1 10.8 - - + -
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Residues in contact with PHE1113 (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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503B LEU* 4.0 8.5 - - + -
506B MET* 3.6 48.2 - - + -
510B LYS* 4.3 1.3 - - + -
828B ILE* 4.9 1.6 - - - +
1105B ILE* 3.1 48.0 - - + -
1108B ALA* 3.7 21.1 - - + -
1109B PRO 3.3 18.2 + - - -
1110B MET* 3.2 24.2 + - + +
1112B PHE* 1.3 87.4 - + - +
1114B GLU* 1.3 61.5 + - - +
1116B THR* 3.4 15.5 - - - +
1118B LEU* 3.9 26.9 - - + +
1121B ILE* 5.0 7.2 - - + -
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Residues in contact with GLU1114 (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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828B ILE* 3.3 48.6 - - + +
829B ASN* 4.5 10.2 + - - +
830B LEU 5.2 1.4 - - - +
1110B MET* 2.9 24.8 + - + +
1111B ARG* 4.1 12.0 + - - +
1113B PHE* 1.3 75.1 - - - +
1115B THR* 1.3 67.3 + - - +
1116B THR 3.8 2.4 - - - +
2502B ADP 2.5 39.8 + - - -
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Residues in contact with THR1115 (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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1111B ARG* 2.7 47.6 + - - +
1112B PHE* 4.0 6.3 - - + -
1114B GLU* 1.3 80.2 - - - +
1116B THR* 1.3 65.8 + - - +
1117B PRO* 3.5 7.3 - - - +
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Residues in contact with THR1116 (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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828B ILE* 4.6 2.4 - - - +
1112B PHE* 2.8 42.8 + - + -
1113B PHE 3.4 14.0 - - - +
1114B GLU 3.4 3.5 - - - +
1115B THR* 1.3 79.1 - - - +
1117B PRO* 1.3 76.4 - - + +
1118B LEU* 3.3 6.6 + - - +
1120B SER* 4.1 4.3 - - - +
1121B ILE* 3.7 34.8 - - + -
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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