Contacts of the strand formed by residues 67 - 72 (chain B) in PDB entry 4M7A
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 VAL 67 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.2 8.7 - - + -
18B GLU 3.8 5.4 - - - +
19B LEU* 3.9 9.6 - - + -
20B LYS* 3.3 16.0 + - - -
36B LEU 5.1 0.9 - - - +
38B LEU* 4.6 11.4 - - + -
62B ILE* 4.0 14.8 - - + -
63B ARG 3.5 13.0 - - - +
64B GLY* 2.9 23.0 + - - +
66B THR* 1.3 75.3 - - - +
68B ARG* 1.3 63.4 + - - +
69B TYR 4.3 6.1 - - - +
70B VAL* 4.3 6.3 - - + -
67C PHE* 4.1 26.0 - - + -
69C ARG* 3.3 17.4 - - + +
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Residues in contact with ARG 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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18B GLU* 2.9 35.5 + - + +
19B LEU 3.8 12.1 + - - -
20B LYS* 3.3 44.1 + - + +
22B ASP* 4.4 2.6 + - - -
66B THR 3.8 2.0 + - - -
67B VAL* 1.3 75.1 - - - +
69B TYR* 1.3 97.4 + - + +
20C LEU* 4.5 2.9 - - - +
21C ARG 5.1 4.2 + - - -
24C ARG* 3.1 40.9 - - - +
67C PHE* 4.8 0.2 - - - -
68C ILE* 3.6 4.9 - - + +
69C ARG* 3.0 29.4 + - - +
72C THR* 4.6 18.6 - - + +
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Residues in contact with TYR 69 (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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17B VAL* 3.8 4.3 - - - +
18B GLU* 3.1 48.9 + - + +
67B VAL* 4.3 1.1 - - - +
68B ARG* 1.3 106.6 - - + +
70B VAL* 1.3 67.2 + - - +
71B TYR* 3.3 27.4 - + + -
20C LEU* 3.2 22.8 - - + +
24C ARG* 3.8 0.9 - - - -
26C LEU* 3.5 28.6 - - + +
46C GLU* 2.6 43.3 + - + +
66C VAL* 3.8 14.8 - - + -
67C PHE 3.4 10.1 - - - -
68C ILE* 4.1 9.2 - - + -
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Residues in contact with VAL 70 (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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7B PHE* 3.7 26.9 - - + -
15B VAL* 4.6 9.9 - - + -
16B VAL 3.8 6.1 - - - +
17B VAL* 4.8 7.6 - - + +
38B LEU* 4.5 13.7 - - + -
67B VAL* 4.3 8.7 - - + -
69B TYR* 1.3 78.4 - - - +
71B TYR* 1.3 65.2 + - - +
72B LEU* 3.8 20.5 + - + +
66C VAL* 3.2 6.5 - - - +
67C PHE* 2.8 63.1 + - + -
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Residues in contact with TYR 71 (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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14B GLU 4.8 0.5 - - - +
15B VAL* 3.9 4.5 - - - +
16B VAL* 2.8 64.9 + - + +
18B GLU* 3.0 34.9 + - + -
24B GLU* 4.7 0.2 - - - -
69B TYR* 3.3 19.1 - + + -
70B VAL* 1.3 73.5 - - - +
72B LEU* 1.3 70.8 + - - +
46C GLU* 4.4 0.9 + - - -
61C ARG* 3.2 44.7 + - + +
62C ARG 5.4 0.2 - - - -
63C SER* 4.0 29.8 - - - -
65C MET 3.7 1.3 - - - +
66C VAL* 4.0 20.6 - - + -
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Residues in contact with LEU 72 (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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6B PHE* 3.8 22.4 - - + -
7B PHE* 5.0 0.4 - - + -
10B LEU* 3.5 32.3 - - + -
15B VAL* 3.4 25.6 - - + -
70B VAL* 4.0 17.3 - - + +
71B TYR* 1.3 87.8 - - - +
73B ASN* 1.3 62.9 + - - +
76B MET* 4.2 15.0 - - + -
77B VAL* 5.1 1.6 - - + -
40C VAL* 5.7 0.4 - - + -
64C GLU* 4.3 4.2 + - - +
65C MET* 2.6 54.7 + - + +
66C VAL 5.4 0.2 - - - -
67C PHE* 4.8 10.3 - - + +
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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