Contacts of the helix formed by residues 100 - 109 (chain B) in PDB entry 4M6W
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 TYR 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66B LEU* 3.9 40.7 - - + +
67B VAL* 4.8 5.0 - - - -
68B ALA* 4.0 33.4 - - + +
96B MET 4.2 18.2 - - - -
97B SER* 3.0 9.4 + - - +
99B GLN* 1.3 88.8 - - + +
101B PHE* 1.3 63.3 + - - +
102B PRO* 3.5 0.9 - - - -
103B ALA* 3.4 16.9 + - - +
104B LEU* 3.4 11.1 + - - +
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Residues in contact with PHE 101 (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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1934A PHE* 4.1 13.2 - - + -
1940A GLU* 5.6 2.2 - - - -
66B LEU* 5.6 1.3 - - - -
91B VAL* 3.7 33.4 - - + -
93B LYS* 4.3 31.6 - - + -
97B SER 3.4 8.1 + - - +
98B GLU 3.3 10.0 + - - +
100B TYR* 1.3 74.5 - - - +
102B PRO* 1.4 77.8 - - + +
104B LEU* 3.0 11.6 + - + +
105B GLN* 2.9 56.1 + - + -
116B LEU* 4.0 16.6 - - + -
118B PRO* 4.1 28.9 - - + -
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Residues in contact with PRO 102 (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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1940A GLU* 4.4 26.7 - - + +
1944A LEU* 6.0 3.3 - - + +
98B GLU 3.6 6.7 - - - +
99B GLN* 3.6 16.8 - - - +
100B TYR 3.6 0.4 - - - -
101B PHE* 1.4 99.0 - - + +
103B ALA* 1.3 54.4 + - - +
105B GLN* 3.7 8.6 + - + +
106B LYS* 3.1 26.9 + - - +
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Residues in contact with ALA 103 (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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99B GLN 5.5 0.4 + - - +
100B TYR* 3.4 11.7 + - + +
101B PHE 3.2 0.6 - - - -
102B PRO* 1.3 77.5 - - - +
104B LEU* 1.3 66.0 + - - +
106B LYS* 3.3 7.3 + - - +
107B PHE* 3.0 25.6 + - - +
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Residues in contact with LEU 104 (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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61B VAL* 4.6 6.7 - - + -
66B LEU* 4.4 12.8 - - + -
72B TYR* 3.7 38.6 + - + +
76B LEU* 4.5 4.5 - - + -
89B VAL* 5.2 3.6 - - + -
91B VAL* 3.7 42.0 - - + -
100B TYR 3.4 9.5 + - - +
101B PHE* 3.0 14.5 + - + +
103B ALA* 1.3 76.9 - - - +
105B GLN* 1.3 58.3 + - - +
107B PHE* 3.3 5.2 + - + +
108B THR* 2.8 58.6 + - - +
116B LEU* 4.0 13.0 - - + -
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Residues in contact with GLN 105 (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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1932A ILE 4.3 1.6 - - - +
1933A LEU* 3.4 30.3 - - + +
1934A PHE* 2.8 55.0 + - - +
1940A GLU* 5.0 2.0 + - - -
1944A LEU* 4.3 16.2 - - + +
101B PHE* 2.9 30.7 + - + +
102B PRO* 3.9 7.6 + - - +
104B LEU* 1.3 74.7 - - - +
106B LYS* 1.3 64.4 + - - +
108B THR 4.6 0.2 - - - +
109B VAL* 3.1 30.1 + - + +
110B LEU* 3.7 3.6 + - + +
116B LEU* 3.5 17.0 - - + +
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Residues in contact with LYS 106 (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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1944A LEU* 6.6 0.2 - - - -
1947A GLU* 3.8 40.1 - - - +
1951A VAL* 6.2 1.8 - - - +
1954A ARG* 4.8 13.5 - - - +
102B PRO 3.1 19.1 + - - +
103B ALA* 3.7 7.6 - - - +
105B GLN* 1.3 76.5 - - - +
107B PHE* 1.3 58.3 + - - +
110B LEU* 3.3 19.7 - - + +
111B ASP* 2.9 55.5 + - - +
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Residues in contact with PHE 107 (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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72B TYR* 5.1 4.7 - + - -
73B ARG* 4.3 32.5 - - + -
76B LEU* 4.0 22.4 - - + -
77B VAL* 4.0 18.4 - - + -
103B ALA 3.0 17.2 + - - +
104B LEU* 3.6 5.2 - - + +
105B GLN 3.2 0.2 - - - -
106B LYS* 1.3 77.6 - - - +
108B THR* 1.3 62.3 + - - +
111B ASP* 3.1 24.0 - - + +
112B LEU* 2.9 62.8 + - + +
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Residues in contact with THR 108 (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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76B LEU* 3.9 10.2 - - + +
89B VAL* 3.6 32.8 - - + +
104B LEU* 2.8 38.5 + - - +
107B PHE* 1.3 75.5 - - - +
109B VAL* 1.3 58.9 + - - +
112B LEU* 3.2 10.5 - - - +
113B GLY 2.9 22.3 + - - -
114B MET* 3.0 26.1 + - + -
115B VAL 4.2 6.5 - - - +
116B LEU* 4.3 14.0 - - + +
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Residues in contact with VAL 109 (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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1931A ARG* 4.3 19.5 - - + +
1932A ILE 4.6 9.2 - - - +
1933A LEU* 3.7 27.6 - - + -
1948A LEU* 6.0 1.1 - - + -
105B GLN* 3.1 23.2 + - + +
108B THR* 1.3 77.3 - - - +
110B LEU* 1.3 64.0 + - + +
113B GLY* 3.2 19.9 - - - -
114B MET 3.8 21.3 - - - +
115B VAL* 4.9 0.2 - - - -
116B LEU* 3.9 30.7 - - + +
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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