Contacts of the helix formed by residues 1017 - 1021 (chain B) in PDB entry 2B7A
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 PRO1017 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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975B ARG 4.9 1.1 - - - +
976B ASP* 3.4 26.5 - - - +
997B LEU* 4.8 8.7 - - + -
1015B GLU 4.3 3.4 - - - +
1016B SER* 1.3 80.0 - - - +
1018B ILE* 1.3 57.4 + - - +
1019B PHE* 3.2 3.4 - - - -
1020B TRP* 3.0 40.4 + - + +
1021B TYR* 3.3 31.7 - - + +
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Residues in contact with ILE1018 (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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1015B GLU* 5.0 7.9 - - - +
1016B SER* 2.8 31.1 + - - +
1017B PRO* 1.3 70.7 - - - +
1019B PHE* 1.3 91.1 + - + +
1020B TRP 3.2 0.7 - - - -
1021B TYR* 3.3 23.5 + - + +
1026B LEU* 3.8 26.2 - - + +
1074B ILE* 4.0 12.8 - - + -
1075B VAL* 3.8 31.0 - - + -
1078B LEU* 3.5 22.9 - - + +
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Residues in contact with PHE1019 (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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1017B PRO 3.1 1.8 + - - -
1018B ILE* 1.3 90.0 - - + +
1020B TRP* 1.3 73.2 + + + +
1021B TYR 3.5 1.3 - - - -
1038B TRP* 5.4 1.0 + - - -
1042B VAL* 4.0 7.6 - - - +
1057B PRO* 4.0 6.7 - - + +
1058B PRO* 3.6 37.5 - - + -
1061B PHE* 3.5 59.2 - + + -
1062B MET* 3.9 20.6 - - + -
1065B ILE* 4.9 2.2 - - + -
1074B ILE* 3.8 26.9 - - + -
1078B LEU* 3.9 21.5 - - + -
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Residues in contact with TRP1020 (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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938B ARG* 6.4 0.2 - - - -
977B LEU 3.1 26.2 - - - +
978B ALA* 3.6 13.6 - - + +
980B ARG* 6.2 2.0 - - - -
1017B PRO* 3.0 28.3 + - + +
1019B PHE* 1.3 89.0 - + + +
1021B TYR* 1.3 62.0 + - + +
1038B TRP* 3.4 12.4 - - - -
1039B SER* 2.7 33.2 + - - +
1042B VAL* 3.4 30.8 - - + +
1043B VAL 4.7 0.2 - - - -
1046B GLU* 2.8 42.9 + - - -
1056B SER* 5.7 0.7 - - - -
1057B PRO* 3.6 12.8 - - + -
1058B PRO* 3.7 39.5 - - + -
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Residues in contact with TYR1021 (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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975B ARG* 3.8 29.9 + - - -
997B LEU* 4.8 3.3 - - - +
1012B GLU* 4.3 9.3 + - - -
1016B SER* 3.5 32.2 + - - -
1017B PRO* 3.3 37.4 - - + +
1018B ILE* 3.3 20.2 + - + +
1019B PHE 3.5 0.7 - - - -
1020B TRP* 1.3 82.2 - - + +
1022B ALA* 1.3 63.5 + - - +
1023B PRO 3.9 0.2 - - - -
1025B SER* 3.9 15.0 - - - -
1026B LEU* 3.5 30.7 - - + +
1031B PHE* 3.5 31.9 - + - -
1038B TRP* 3.1 15.5 + - - -
1039B SER* 4.6 4.0 - - - -
1082B LEU* 4.4 3.1 - - - +
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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