Contacts of the strand formed by residues 86 - 92 (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 LYS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1926A ILE* 4.6 18.3 + - - +
1927A GLY* 6.3 0.7 - - - -
1929A GLY* 5.8 2.4 - - - -
1931A ARG* 4.4 14.8 - - - +
55B ARG 2.9 19.8 + - - +
56B CYS* 3.3 22.2 - - + -
57B CYS* 3.0 25.4 + - - -
84B ASN 4.4 2.9 - - - +
85B LEU* 1.3 71.7 - - - +
87B GLY* 1.3 61.3 + - - +
88B ILE* 3.9 22.1 - - + +
115B VAL* 4.1 13.9 - - - +
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Residues in contact with GLY 87 (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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57B CYS* 3.6 18.2 - - - -
59B LEU* 4.6 4.0 - - - -
79B VAL* 3.9 14.4 - - - +
85B LEU 3.8 4.0 + - - -
86B LYS* 1.3 77.1 + - - +
88B ILE* 1.3 66.7 + - - +
114B MET* 3.7 30.1 - - - +
115B VAL* 4.0 1.2 + - - +
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Residues in contact with ILE 88 (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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1926A ILE* 4.6 7.6 - - + -
52B LEU* 4.2 10.8 - - + -
56B CYS* 4.4 5.6 - - - -
57B CYS 2.9 20.5 + - - +
58B ILE* 3.4 14.3 - - + +
59B LEU* 3.2 20.0 + - - +
86B LYS* 3.9 21.3 - - + +
87B GLY* 1.3 80.2 - - - +
89B VAL* 1.3 63.1 + - - +
90B VAL* 3.8 2.2 + - + +
115B VAL* 3.6 35.7 - - + -
117B LEU* 5.2 5.6 - - + -
132B LEU* 3.7 40.8 - - + -
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Residues in contact with VAL 89 (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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59B LEU* 3.3 21.5 - - + +
61B VAL* 3.9 22.9 - - + -
76B LEU* 3.7 28.3 - - + -
88B ILE* 1.3 74.5 - - - +
90B VAL* 1.3 64.9 + - - +
104B LEU* 5.2 2.5 - - + -
108B THR* 3.6 24.5 - - + +
114B MET* 4.1 8.7 - - - -
115B VAL 2.6 14.5 + - - +
116B LEU* 3.2 22.1 - - + -
117B LEU* 2.8 25.8 + - - +
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Residues in contact with VAL 90 (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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58B ILE* 3.9 25.6 - - + -
59B LEU 2.8 9.7 + - - +
60B TYR* 3.4 24.9 - - + -
61B VAL* 2.8 26.9 + - - +
88B ILE 4.3 2.9 - - - +
89B VAL* 1.3 77.7 - - - +
91B VAL* 1.3 62.2 + - - +
117B LEU* 3.5 31.0 - - + +
119B VAL* 4.2 14.4 - - + -
125B ALA* 4.6 4.7 - - + -
128B LEU* 4.1 18.2 - - + -
129B VAL* 5.4 4.9 - - + -
132B LEU* 5.1 2.2 - - + -
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Residues in contact with VAL 91 (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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60B TYR* 5.6 0.4 - - - -
61B VAL* 3.4 12.8 - - + +
66B LEU* 3.8 17.5 - - + -
90B VAL* 1.3 73.5 - - - +
92B GLU* 1.3 74.9 + - - +
93B LYS* 3.3 0.4 + - - -
101B PHE* 3.7 29.2 - - + -
104B LEU* 3.7 24.2 - - + -
116B LEU* 3.6 22.7 - - + -
117B LEU 2.9 16.9 + - - +
118B PRO* 4.0 2.0 - - + -
119B VAL* 2.9 31.4 + - - +
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Residues in contact with GLU 92 (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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60B TYR* 2.7 38.0 + - + +
61B VAL 2.9 11.4 + - - +
62B THR* 3.4 16.5 - - - +
63B GLU* 3.1 41.3 + - + +
91B VAL* 1.3 79.9 - - - +
93B LYS* 1.3 60.0 + - - +
94B THR* 3.9 2.0 - - - +
97B SER* 3.0 18.0 + - - -
119B VAL* 3.2 9.4 - - + +
120B ALA 4.4 11.4 - - - +
121B SER* 5.1 0.9 - - - -
122B GLN* 3.9 21.4 + - - +
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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