Contacts of the helix formed by residues 46 - 56 (chain B) in PDB entry 3I7P
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 LEU 46 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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841A ALA 3.4 13.2 + - - +
842A GLU* 4.8 14.5 - - + +
843A PRO* 5.5 0.2 - - - +
871A TYR* 5.1 2.9 - - - +
910A MET* 3.9 38.8 - - + -
926A LEU* 5.0 7.2 - - + -
45B SER* 1.3 74.8 - - - +
47B VAL* 1.3 55.9 + - - +
48B TYR 3.4 0.7 - - - -
49B TYR* 3.0 25.0 - - + +
50B LEU* 2.6 41.1 + - + +
53B ARG* 5.3 6.1 - - - +
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Residues in contact with VAL 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
812A TYR* 4.8 4.0 - - + -
814A LEU* 4.6 12.6 - - + -
836A VAL* 3.2 33.7 - - + -
843A PRO* 4.1 24.2 - - + -
869A ALA* 5.0 2.5 - - + -
871A TYR* 4.4 17.3 - - + +
45B SER* 3.1 19.5 - - - +
46B LEU* 1.3 75.8 - - + +
48B TYR* 1.3 66.6 + - + +
49B TYR 2.8 9.1 + - - -
50B LEU* 4.1 5.2 - - - +
51B LYS* 2.4 52.1 + - - +
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Residues in contact with TYR 48 (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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787A GLU* 4.8 7.9 - - - -
810A ASN* 5.7 0.5 + - - -
812A TYR* 3.2 29.2 + + - -
836A VAL* 3.0 27.2 + - + +
838A PRO* 3.2 41.6 - - + +
45B SER* 2.7 46.9 + - - +
46B LEU 3.4 0.2 - - - -
47B VAL* 1.3 83.3 - - + +
49B TYR* 1.3 54.5 + - + +
51B LYS* 4.2 6.0 - - - +
52B ASN* 2.9 34.5 + - - +
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Residues in contact with TYR 49 (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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45B SER 4.1 12.3 - - - -
46B LEU* 3.0 31.4 - - + +
48B TYR* 1.3 81.6 - - + +
50B LEU* 1.3 56.4 + - - +
51B LYS 3.1 0.4 - - - -
52B ASN* 3.6 17.9 - - + -
53B ARG* 2.5 71.5 + - + +
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Residues in contact with LEU 50 (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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871A TYR* 4.0 15.3 - - + -
910A MET* 3.9 17.9 - - + -
912A LEU* 3.8 36.3 - - + -
913A TYR* 5.6 2.9 - - - +
926A LEU* 4.6 7.4 - - + -
46B LEU* 2.6 23.2 + - + +
47B VAL* 3.3 4.5 + - - +
49B TYR* 1.3 74.9 - - - +
51B LYS* 1.3 53.1 + - + +
52B ASN 2.8 0.2 - - - -
53B ARG* 3.3 29.3 + - - +
54B GLU* 2.3 51.9 + - - +
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Residues in contact with LYS 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
722A ARG* 3.3 45.3 + - - +
787A GLU* 4.3 3.8 - - - +
789A HIS* 3.9 1.0 - - - -
812A TYR* 2.5 41.9 - - + +
813A ALA 5.6 1.1 - - - -
814A LEU* 3.0 33.4 - - - +
47B VAL* 2.4 33.2 - - - +
48B TYR* 4.2 7.0 - - + +
50B LEU* 1.3 69.5 - - + +
52B ASN* 1.3 55.8 + - - +
54B GLU* 2.4 40.7 - - - +
55B VAL* 3.7 8.5 + - - +
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Residues in contact with ASN 52 (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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48B TYR 2.9 20.7 + - - +
49B TYR* 3.6 23.8 - - + +
50B LEU 2.8 1.4 + - - -
51B LYS* 1.3 78.1 - - - +
53B ARG* 1.3 56.8 + - + +
54B GLU 2.3 15.2 + - - -
55B VAL* 2.8 24.9 + - - +
56B ARG* 3.1 10.5 + - - -
57B LEU 5.4 9.6 + - - +
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Residues in contact with ARG 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
926A LEU* 4.9 9.3 - - - +
953A TRP* 5.1 14.4 - - - -
970A ASN* 6.0 1.6 - - - -
1003A PHE* 4.2 30.5 - - + -
1033A VAL* 4.3 1.7 - - - +
46B LEU* 4.8 6.9 + - - +
49B TYR* 2.5 66.0 + - + +
50B LEU* 3.5 31.1 - - + +
52B ASN* 1.3 74.3 - - + +
54B GLU* 1.4 63.2 + - - +
56B ARG* 3.4 15.5 + - - +
57B LEU 5.1 3.1 - - - +
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Residues in contact with GLU 54 (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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358A PRO* 4.7 0.3 - - - +
360A VAL* 4.5 16.7 - - + +
722A ARG* 6.0 5.8 - - - -
913A TYR* 5.3 4.7 + - - -
1003A PHE* 5.5 1.3 - - - -
1005A ASN* 3.3 28.9 + - - +
1033A VAL* 3.3 16.1 - - - +
50B LEU* 2.3 47.4 + - - +
51B LYS* 2.4 33.8 + - + +
52B ASN 2.3 13.7 + - - -
53B ARG* 1.4 70.8 - - - +
55B VAL* 1.3 61.0 + - + +
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Residues in contact with VAL 55 (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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327A ARG* 4.1 2.7 + - - +
328A LEU* 3.7 21.5 - - + -
358A PRO* 3.9 21.4 - - + +
360A VAL* 5.2 4.7 - - + -
380A GLY 5.0 1.8 - - - +
381A ALA* 3.6 29.8 - - + -
382A PHE* 5.4 6.3 - - + -
1033A VAL* 2.8 14.9 - - - +
51B LYS 4.4 7.0 - - - +
52B ASN* 2.8 25.6 + - - +
54B GLU* 1.3 78.4 - - + +
56B ARG* 1.3 88.9 + - - +
57B LEU 5.4 0.7 - - - -
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Residues in contact with ARG 56 (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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60A LYS* 5.6 6.7 - - - +
327A ARG* 3.3 33.0 + - - +
972A PHE* 4.7 22.0 - - - -
1003A PHE* 5.1 9.8 - - - +
1033A VAL* 2.8 25.6 - - + -
1034A ASN* 5.5 2.5 - - - +
52B ASN 3.1 6.7 + - - -
53B ARG* 3.8 11.2 - - - +
54B GLU 3.4 0.8 - - - -
55B VAL* 1.3 101.0 - - - +
57B LEU* 1.3 117.5 + - + +
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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