Contacts of the strand formed by residues 79 - 85 (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 ARG 79 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ILE 3.9 0.5 - - - +
73B LYS* 5.8 0.2 - - - -
74B MET* 3.1 34.7 + - - +
77B ALA* 3.2 10.2 - - + +
78B GLN* 1.3 79.2 + - - +
80B SER* 1.3 69.6 + - - +
81B TYR* 3.3 26.2 - - + +
199B ARG* 3.9 9.7 - - - +
204B LEU* 3.0 51.5 + - + +
229B ASP* 2.5 55.1 + - - -
233B LEU* 3.5 26.3 - - + +
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Residues in contact with SER 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LEU* 4.2 6.8 - - - +
72B ILE 3.3 6.5 - - - -
73B LYS* 3.6 28.2 - - - +
79B ARG* 1.3 80.3 - - - +
81B TYR* 1.3 65.6 + - - +
204B LEU* 5.5 0.9 - - - +
210B PRO* 3.7 33.8 - - - +
211B VAL* 3.9 4.9 + - - +
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Residues in contact with TYR 81 (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 3.5 0.7 - - - +
71B LEU* 3.6 3.6 - - - +
72B ILE* 2.7 54.5 + - + +
74B MET* 4.3 1.1 - - + -
79B ARG* 3.3 29.1 - - + +
80B SER* 1.3 77.3 - - - +
82B ILE* 1.3 62.1 + - - +
83B LEU* 3.6 18.6 - - + -
204B LEU* 4.8 3.4 - - + -
210B PRO* 4.0 1.3 - - - -
211B VAL* 3.8 24.2 - - + -
213B VAL* 4.6 0.7 - - + -
225B PHE* 5.0 3.6 - + - -
226B CYS* 3.3 39.3 - - + -
229B ASP* 2.5 32.2 + - + -
230B THR* 2.7 36.3 + - - -
233B LEU* 4.1 0.2 - - - +
253B MET* 4.1 4.0 - - + -
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Residues in contact with ILE 82 (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 ILE* 3.7 31.2 - - + -
69B ALA* 4.3 5.2 - - + -
70B SER 3.3 7.6 - - - +
71B LEU* 4.5 2.9 - - + -
81B TYR* 1.3 74.7 - - - +
83B LEU* 1.3 59.4 + - - +
84B THR 4.0 0.2 + - - -
98B MET* 3.9 30.5 - - + -
102B GLN* 4.0 27.1 - - + +
210B PRO* 3.5 26.7 - - + -
211B VAL 2.9 13.4 + - - +
212B VAL* 4.0 15.4 - - + +
213B VAL* 2.7 33.3 + - - +
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Residues in contact with LEU 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ALA* 3.3 1.9 - - - -
70B SER 2.7 37.8 + - - -
72B ILE* 3.9 17.7 - - + -
81B TYR* 3.6 12.6 - - + -
82B ILE* 1.3 77.9 - - - +
84B THR* 1.3 61.9 + - - +
213B VAL* 3.4 4.3 - - + +
218B GLY 3.7 9.0 - - - +
222B SER* 4.0 31.4 - - - +
223B GLY* 4.1 2.5 - - - +
226B CYS* 3.5 27.4 - - + -
257B ARG* 3.6 19.7 + - - -
260B LEU* 3.7 33.0 - - + -
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Residues in contact with THR 84 (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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67B ILE* 4.4 5.9 - - - +
68B ASN 2.6 24.0 + - - -
69B ALA* 3.4 14.4 - - - +
82B ILE* 4.8 0.2 - - - -
83B LEU* 1.3 78.4 - - - +
85B GLN* 1.3 73.9 + - - +
95B PHE* 3.9 12.1 - - + -
98B MET* 4.0 6.9 - - + +
212B VAL* 3.9 20.0 - - + -
213B VAL 3.0 6.4 + - - +
214B HIS* 3.1 30.0 - - + +
218B GLY* 3.1 19.5 - - - -
257B ARG* 4.0 3.4 - - - +
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Residues in contact with GLN 85 (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 2.8 26.1 + - - -
45B ARG* 2.9 33.9 + - + +
46B TYR* 4.4 1.6 + - + -
49B VAL* 6.0 0.5 - - - +
67B ILE* 6.3 1.0 - - + +
68B ASN* 3.3 35.4 + - + +
84B THR* 1.3 91.5 + - - +
86B GLY* 1.3 72.9 + - - +
87B PRO* 3.1 10.4 - - + +
88B LEU* 3.7 15.0 - - - +
91B THR* 4.6 6.7 + - - +
95B PHE* 4.8 0.9 - - - -
214B HIS* 4.1 1.9 - - - +
215B CYS 3.9 0.7 - - - -
216B SER 3.7 13.7 - - - +
217B ALA* 4.0 15.0 - - - +
218B GLY 4.1 0.2 - - - +
257B ARG* 3.9 3.8 - - - +
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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