Contacts of the helix formed by residues 1042 - 1047 (chain B) in PDB entry 5B2R
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 ILE1042 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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921B LEU* 3.7 20.0 - - + -
997B LEU* 3.9 7.9 - - + -
1001B TYR* 3.5 36.8 + - + -
1004B LEU* 3.7 22.0 - - + -
1008B PHE* 5.9 2.7 - - + -
1038B PHE* 3.0 43.0 + - + +
1039B TYR* 3.6 20.6 - - + +
1040B SER 3.7 0.8 - - - -
1041B ASN* 1.3 77.7 - - - +
1043B MET* 1.3 75.8 + - + +
1044B ASN 3.3 0.6 + - - -
1045B PHE* 3.3 22.3 + - - -
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Residues in contact with MET1043 (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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921B LEU* 5.1 0.4 - - + -
962B LEU* 3.5 43.5 - - + +
965B ASP* 6.5 1.6 - - + -
966B PHE* 5.5 6.3 - - + +
969B ASP* 6.0 1.8 - - - +
970B PHE* 5.9 0.2 - - - -
993B VAL* 4.2 9.0 - - - -
997B LEU* 3.7 27.4 - - + -
1040B SER 5.5 0.2 + - - -
1041B ASN 3.1 1.2 - - - -
1042B ILE* 1.3 98.9 - - + +
1044B ASN* 1.3 64.6 + - - +
1045B PHE* 3.2 6.4 + - - -
1046B PHE* 3.6 41.7 + - + +
1047B LYS* 4.7 8.9 + - - +
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Residues in contact with ASN1044 (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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1040B SER 4.7 1.6 - - - +
1041B ASN* 2.5 54.4 + - - +
1042B ILE 3.3 0.8 - - - -
1043B MET* 1.3 79.7 - - - +
1045B PHE* 1.3 58.6 + - - +
1046B PHE 3.1 0.2 - - - -
1047B LYS* 2.9 39.2 + - - +
1050B ILE* 3.9 26.6 - - + +
1052B LEU* 3.7 14.8 - - - +
1060B ARG* 3.7 16.2 - - - +
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Residues in contact with PHE1045 (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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996B ALA 4.1 16.4 - - - -
997B LEU* 4.0 22.4 - - + -
1000B LYS* 3.9 23.1 - - + -
1001B TYR* 3.8 18.9 + + - +
1041B ASN 4.9 0.2 + - - -
1042B ILE 3.3 23.5 + - - -
1043B MET* 4.2 3.1 - - - -
1044B ASN* 1.3 77.6 - - - +
1046B PHE* 1.3 107.3 + + - +
1047B LYS 3.5 2.3 + - - +
1060B ARG* 3.5 20.8 - - - +
1064B GLU* 3.1 47.8 - - + +
1073B VAL* 4.4 7.9 - - + -
1074B TRP* 4.7 4.4 - - + -
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Residues in contact with PHE1046 (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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966B PHE* 3.9 31.6 - + - -
970B PHE* 3.4 29.3 - + + -
992B VAL* 5.5 0.4 - - + -
993B VAL* 4.5 14.4 - - + -
996B ALA* 3.7 14.8 - - + -
1043B MET* 3.6 34.9 + - + +
1044B ASN 3.0 1.2 + - - -
1045B PHE* 1.3 111.1 - + - +
1047B LYS* 1.3 59.1 + - - +
1048B THR* 4.0 2.6 + - - -
1074B TRP* 3.4 62.2 + + - +
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Residues in contact with LYS1047 (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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969B ASP* 3.7 35.7 + - - -
970B PHE* 3.8 20.6 - - + -
1043B MET* 4.8 10.1 - - - +
1044B ASN* 2.9 16.2 + - - +
1045B PHE 4.0 1.9 - - - +
1046B PHE* 1.3 80.0 - - - +
1048B THR* 1.3 63.4 + - - +
1049B GLU 4.3 7.9 - - - +
1050B ILE* 3.5 35.9 - - + +
1060B ARG* 3.5 24.9 - - - +
1061B PRO 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