Contacts of the strand formed by residues 60 - 68 (chain B) in PDB entry 6J7Z
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 ILE 60 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48B LEU* 3.7 34.8 - - + -
49B GLU 3.8 4.0 - - - +
50B MET* 4.2 3.1 - - + -
59B GLN* 1.3 74.9 + - - +
61B ILE* 1.3 62.6 + - - +
62B GLU 3.6 24.0 - - - +
63B MET* 4.6 7.6 - - + -
83B ILE* 3.2 16.5 - - + +
85B GLN* 3.0 21.6 + - - +
117B LEU* 4.7 15.1 - - + +
150B PHE* 4.1 31.9 - - + +
151B LEU* 4.4 11.0 - - + -
154B TYR* 4.2 17.8 - - + -
155B MET* 5.1 4.5 - - + -
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Residues in contact with ILE 61 (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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49B GLU 2.8 22.8 + - - +
50B MET 3.7 9.2 - - - +
51B THR* 3.6 23.6 - - + +
59B GLN 3.7 0.4 + - - -
60B ILE* 1.3 73.1 - - - +
62B GLU* 1.3 58.9 + - - +
82B ILE* 3.3 10.7 - - - +
83B ILE* 2.7 32.5 + - - -
85B GLN* 3.6 26.0 - - + -
90B LEU* 4.4 5.8 - - + -
101B HIS* 3.6 32.5 - - + +
106B LEU* 3.7 20.9 - - + -
107B THR* 6.0 0.7 - - - +
110B VAL* 3.6 23.5 - - + +
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Residues in contact with GLU 62 (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 LEU* 3.4 3.6 - - - -
49B GLU* 2.9 48.6 + - + +
60B ILE* 3.6 6.4 - - - +
61B ILE* 1.3 79.0 - - - +
63B MET* 1.3 65.9 + - - +
80B ASN* 4.1 11.0 - - - +
81B LEU 3.3 13.7 - - - +
82B ILE* 3.9 11.6 - - + +
83B ILE* 4.7 0.7 - - - -
106B LEU* 4.0 13.9 - - + +
195B ARG* 2.7 45.4 + - - -
196B ALA* 3.1 31.8 + - + -
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Residues in contact with MET 63 (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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46B VAL* 4.0 17.7 - - + -
47B ASP 3.4 5.4 - - - +
48B LEU* 3.5 19.7 - - + -
60B ILE* 4.6 7.2 - - + -
62B GLU* 1.3 77.9 - - - +
64B ALA* 1.3 64.4 + - - +
80B ASN* 3.5 2.1 - - - +
81B LEU 2.9 34.1 + - - +
83B ILE* 4.7 5.2 - - + -
124B PHE* 3.4 52.9 - - + -
151B LEU* 3.8 20.0 - - + -
155B MET* 3.8 22.7 - - - +
158B PHE* 4.0 17.0 - - + -
196B ALA* 3.9 2.5 - - - -
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Residues in contact with ALA 64 (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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46B VAL* 3.3 6.6 - - - +
47B ASP 3.0 31.5 + - - +
63B MET* 1.3 76.9 - - - +
65B CYS* 1.3 62.0 + - - +
79B PRO 3.6 7.2 - - - +
80B ASN* 3.8 8.3 - - - +
124B PHE* 4.3 1.6 - - - -
196B ALA* 3.6 6.7 - - + +
197B LEU* 3.5 45.5 - - + +
200B ILE* 4.5 5.0 - - + +
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Residues in contact with CYS 65 (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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44B VAL* 3.7 25.8 - - - -
45B TRP 3.2 12.1 - - - +
46B VAL* 3.9 9.2 - - + -
64B ALA* 1.3 76.9 - - - +
66B LEU* 1.3 75.3 + - - +
77B GLU* 4.9 0.2 - - - +
78B GLY* 2.9 27.2 + - - +
79B PRO 3.5 5.2 + - - +
124B PHE* 3.6 23.1 - - + -
127B PHE* 4.0 22.4 - - + -
128B VAL* 4.3 6.5 - - - -
158B PHE* 4.7 1.6 - - - -
197B LEU* 5.5 0.9 - - - +
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Residues in contact with LEU 66 (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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44B VAL* 3.6 0.3 - - - -
45B TRP* 2.9 38.6 + - + +
65B CYS* 1.3 84.5 - - - +
67B ILE* 1.3 72.6 + - - +
68B THR 4.2 0.2 - - - -
74B ILE* 4.3 20.4 - - + -
76B ALA 3.5 4.7 - - - +
77B GLU* 3.7 39.7 - - + +
78B GLY 4.4 0.7 - - - +
197B LEU* 4.1 11.2 - - + -
200B ILE* 3.9 24.7 - - + -
201B SER* 4.6 9.4 - - - +
204B ILE* 3.7 27.1 - - + -
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Residues in contact with ILE 67 (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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42B ARG* 4.1 29.4 - - + +
43B MET 3.4 4.9 - - - +
44B VAL* 3.6 34.8 - - + -
65B CYS* 4.4 0.4 - - - -
66B LEU* 1.3 80.6 - - - +
68B THR* 1.3 64.8 + - - +
74B ILE* 3.5 2.4 - - - -
75B LEU* 2.6 35.5 + - + -
76B ALA* 2.9 22.5 + - + +
127B PHE* 3.4 33.4 - - + -
128B VAL* 4.6 3.8 - - + -
131B GLN* 3.9 13.0 - - + +
132B THR* 4.1 10.3 - - + -
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Residues in contact with THR 68 (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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42B ARG* 3.3 9.4 - - - +
43B MET* 2.9 33.4 + - - +
45B TRP* 3.0 37.8 + - + +
67B ILE* 1.3 79.2 - - - +
69B ASP* 1.3 70.9 + - - +
72B LEU* 3.9 13.6 - - - +
73B ASN 3.1 11.2 - - - -
74B ILE* 4.0 15.0 - - + -
75B LEU* 3.9 5.4 - - - -
204B ILE* 3.7 20.4 - - + -
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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