Contacts of the strand formed by residues 66 - 74 (chain B) in PDB entry 2CM3
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 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34B VAL* 3.8 19.5 - - + -
35B ALA* 3.2 25.3 - - + +
40B ASN* 3.5 36.3 - - + +
43B ARG* 3.1 37.4 + - + -
44B ASN* 2.6 30.9 + - - -
51B PRO* 3.1 30.5 - - + +
56B ARG* 3.9 11.7 - - - +
59B LEU* 3.6 5.0 - - - +
64B ASN* 3.0 17.7 + - - +
65B ASP* 1.3 84.1 + - - +
67B ILE* 1.3 72.6 + - - +
68B ASN* 3.5 15.7 - - - -
94B HIS* 4.6 1.7 + - - -
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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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43B ARG* 5.5 2.2 - - - -
51B PRO* 4.3 1.4 - - - +
56B ARG* 4.9 0.7 - - - +
57B ILE* 3.3 30.3 + - + +
59B LEU* 3.8 23.1 - - + -
65B ASP 3.9 0.2 + - - -
66B TYR* 1.3 91.1 - - - +
68B ASN* 1.3 69.7 + - - +
69B ALA* 2.8 19.7 + - + +
84B THR* 4.4 3.8 - - - +
85B GLN* 6.3 1.3 - - + +
91B THR* 5.1 7.2 - - + +
94B HIS* 3.9 28.9 - - + +
95B PHE* 3.9 13.2 - - + +
98B MET* 3.9 26.0 - - + -
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Residues in contact with ASN 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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43B ARG 4.1 3.6 + - - +
44B ASN* 3.2 22.1 + - - +
46B TYR 4.9 0.2 + - - -
49B VAL* 2.9 27.1 + - - +
50B SER* 4.0 0.2 - - - +
51B PRO* 3.6 12.0 - - - +
66B TYR* 3.5 16.7 + - - +
67B ILE* 1.3 71.7 - - - +
69B ALA* 1.3 52.0 + - - +
84B THR* 2.6 26.0 + - - -
85B GLN* 3.3 40.3 + - - +
257B ARG* 2.9 34.6 + - - +
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Residues in contact with ALA 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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51B PRO* 3.7 3.9 - - - +
56B ARG* 3.3 6.8 - - - +
57B ILE* 2.8 32.8 + - + -
67B ILE* 2.8 11.3 + - + -
68B ASN* 1.3 74.2 + - - +
70B SER* 1.3 63.7 + - - +
82B ILE* 4.3 1.1 - - + -
83B LEU 3.3 6.7 - - - +
84B THR* 3.4 15.0 - - - +
98B MET* 3.4 33.2 - - + -
257B ARG* 4.0 1.3 - - - +
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Residues in contact with SER 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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51B PRO* 3.3 17.0 - - - +
55B SER* 3.6 7.9 - - - -
57B ILE* 4.2 4.9 - - - -
69B ALA* 1.3 73.1 - - - +
71B LEU* 1.3 59.5 + - - +
72B ILE* 3.2 8.0 - - - +
82B ILE* 3.3 2.8 - - - -
83B LEU 2.7 37.3 + - - -
256B PHE 3.6 19.9 + - - -
257B ARG* 2.9 40.2 + - - +
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Residues in contact with LEU 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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55B SER* 2.9 25.4 + - - +
57B ILE* 3.7 20.0 - - + +
70B SER* 1.3 70.4 - - - +
72B ILE* 1.3 63.9 + - - +
73B LYS* 4.4 15.5 - - + +
80B SER* 4.2 15.3 - - - +
81B TYR 3.6 6.3 - - - +
82B ILE* 4.5 2.0 - - + -
102B GLN* 6.1 2.2 - - - +
210B PRO* 3.9 27.8 - - + -
256B PHE* 3.4 22.3 - - + +
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Residues in contact with ILE 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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70B SER* 3.2 31.2 - - - +
71B LEU* 1.3 74.0 - - - +
73B LYS* 1.3 58.5 + - - +
74B MET* 3.7 29.4 + - + -
79B ARG 3.9 0.9 - - - +
80B SER* 3.3 3.8 - - - -
81B TYR* 2.7 45.7 + - + +
83B LEU* 3.9 26.5 - - + -
226B CYS* 5.9 0.7 - - + -
253B MET* 4.5 16.2 - - + +
256B PHE* 3.6 21.3 - - + -
257B ARG* 4.0 10.1 - - + -
260B LEU* 4.7 7.0 - - + -
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Residues in contact with LYS 73 (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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71B LEU* 3.8 18.3 + - + -
72B ILE* 1.3 72.8 - - - +
74B MET* 1.3 62.5 + - - +
75B GLU* 2.7 49.8 + - - +
78B GLN* 5.6 2.2 - - - +
79B ARG 5.8 0.2 - - - -
80B SER* 3.6 20.4 - - - +
252B GLU* 5.2 0.9 - - - +
256B PHE* 3.4 32.1 - - + -
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Residues in contact with MET 74 (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 ILE* 3.8 16.4 - - + -
73B LYS* 1.3 76.8 + - - +
75B GLU* 1.3 59.8 + - - +
76B GLU 3.6 1.1 - - - +
77B ALA* 4.3 15.7 - - + +
78B GLN* 3.0 22.3 + - - -
79B ARG 3.1 25.2 + - - +
81B TYR* 4.3 1.3 - - + -
230B THR* 3.8 9.6 - - + +
234B LEU* 6.4 0.2 - - + -
249B VAL* 3.9 15.7 - - + +
252B GLU* 3.7 28.3 - - + -
253B MET* 3.4 55.6 - - + -
256B PHE* 4.6 3.1 - - - -
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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