Contacts of the helix formed by residues 1001 - 1005 (chain B) in PDB entry 1FVR
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 PRO1001 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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963B ARG 4.9 7.0 - - - +
964B ASP* 3.6 18.2 - - + +
968B ARG* 3.2 30.3 - - - +
999B ARG 4.0 5.8 - - - +
1000B LEU* 1.4 89.6 - - + +
1002B VAL* 1.3 64.0 + - - +
1003B ARG 3.2 2.9 - - - -
1004B TRP* 3.0 21.1 + - + +
1005B MET* 3.3 20.3 + - + +
1015B TYR* 5.7 1.6 - - + +
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Residues in contact with VAL1002 (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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1000B LEU* 2.8 30.5 + - + +
1001B PRO* 1.3 70.7 - - - +
1003B ARG* 1.3 62.0 + - - +
1004B TRP 3.1 1.4 + - - -
1005B MET* 3.2 25.4 + - - +
1010B LEU* 3.7 20.4 - - + +
1044B CYS* 4.0 24.5 - - + -
1047B LEU* 3.9 26.9 - - + +
1048B TYR* 3.8 33.2 - - + +
1051B LEU* 5.2 2.9 - - - +
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Residues in contact with ARG1003 (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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1001B PRO 3.1 1.4 + - - -
1002B VAL* 1.3 75.6 - - + +
1004B TRP* 1.3 82.5 + - + +
1005B MET 3.6 0.7 - - - -
1022B TRP* 5.3 1.0 + - - -
1026B VAL* 3.6 14.6 - - - +
1037B THR* 4.5 12.8 - - - +
1038B PRO* 3.0 32.2 + - + +
1039B TYR* 3.2 52.7 + - + +
1040B CYS* 4.9 0.6 - - - +
1041B GLY 5.1 0.6 - - - +
1042B MET 3.0 21.8 + - - -
1043B THR* 4.4 6.1 - - - +
1044B CYS* 4.5 15.2 - - - -
1047B LEU* 3.7 18.8 - - + +
1117B ASP* 5.1 1.2 + - - -
1120B ALA* 3.1 39.6 + - - +
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Residues in contact with TRP1004 (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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911B LEU* 6.2 2.2 - - + -
964B ASP* 5.4 2.5 - - - +
965B LEU 3.2 28.0 - - - +
966B ALA* 3.2 8.5 - - + +
968B ARG* 3.3 36.8 - - - +
1001B PRO* 3.0 17.7 + - + +
1003B ARG* 1.3 103.0 - - + +
1005B MET* 1.3 62.9 + - + +
1022B TRP* 3.6 5.5 - - - -
1023B SER* 2.7 37.7 + - - +
1026B VAL* 3.6 28.2 - - + +
1027B LEU 4.4 0.2 - - - -
1030B GLU* 2.7 44.2 + - - -
1037B THR* 5.8 0.9 - - + -
1038B PRO* 3.6 23.3 - - + -
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Residues in contact with MET1005 (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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963B ARG 5.6 1.3 - - - +
1000B LEU* 3.8 35.9 - - + -
1001B PRO* 3.3 26.0 - - + +
1002B VAL* 3.2 16.8 + - - +
1003B ARG 5.2 0.5 - - - -
1004B TRP* 1.3 78.6 - - + +
1006B ALA* 1.3 64.1 + - - +
1007B ILE 3.9 0.2 + - - -
1009B SER* 3.5 34.5 - - - +
1010B LEU* 3.7 31.2 - - + +
1013B SER* 5.6 0.2 - - - -
1015B TYR* 3.5 28.7 - - + +
1022B TRP* 3.3 13.2 + - - -
1023B SER* 4.7 0.9 - - - -
1048B TYR* 4.8 1.1 - - - +
1051B LEU* 4.6 2.4 - - - +
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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