Contacts of the strand formed by residues 66 - 73 (chain M) in PDB entry 6E0P
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 GLY 66 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60M LYS 3.6 1.0 - - - +
61M GLN* 3.4 7.1 - - - -
62M THR* 3.0 34.7 + - - -
63M PRO* 5.0 0.8 - - - -
64M ARG 3.6 2.0 - - - +
65M GLN* 1.3 80.9 - - - +
67M LEU* 1.3 62.1 + - - -
68M GLU* 3.9 2.3 + - - +
245M TYR* 5.1 11.9 - - - -
257M GLY 5.4 2.5 - - - -
258M SER* 5.3 7.0 - - - -
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Residues in contact with LEU 67 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M VAL* 3.7 16.6 - - + -
60M LYS 3.4 1.1 - - - -
61M GLN* 3.7 35.4 - - + +
65M GLN 3.8 2.3 + - - +
66M GLY* 1.3 72.9 - - - -
68M GLU* 1.3 65.3 + - - +
117M TYR* 4.9 5.8 - - + -
132M TRP* 5.1 1.3 - - + -
194M TYR* 6.0 1.1 - - + -
196M GLN* 4.7 2.7 - - - +
202M PRO* 4.8 13.5 - - + -
245M TYR* 3.7 47.6 - - + -
256M PHE* 3.5 53.6 + - + +
257M GLY 4.9 2.6 + - - +
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Residues in contact with GLU 68 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59M VAL* 3.4 6.4 - - - -
60M LYS* 2.7 55.1 + - + +
62M THR* 5.7 1.6 - - - -
65M GLN* 2.9 43.3 - - - +
66M GLY 4.7 2.2 - - - +
67M LEU* 1.3 80.0 - - - +
69M TRP* 1.3 64.5 + - - +
83M ASN* 5.6 2.5 - - - +
85M LYS* 3.7 30.9 + - - -
86M PHE* 3.9 17.1 - - + -
256M PHE* 4.2 2.0 - - - +
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Residues in contact with TRP 69 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M GLN* 2.5 28.1 + - + +
58M TRP 3.8 9.9 - - - -
59M VAL* 4.6 7.6 - - + +
68M GLU* 1.3 71.5 - - - +
70M ILE* 1.3 62.7 + - - +
71M GLY* 3.5 21.9 + - - -
72M TYR* 3.5 33.4 - + - -
81M LYS* 4.2 13.5 - - + -
82M TYR 4.3 2.9 - - - -
83M ASN* 3.0 49.8 + - + +
86M PHE* 4.1 3.1 - - - -
129M LEU* 5.6 3.4 - - + -
247M LEU* 6.2 0.7 - - + -
252M SER 3.3 24.9 - - - -
253M PRO* 4.0 4.9 - - + -
254M TYR* 3.3 57.9 + + + +
256M PHE* 4.0 14.1 - + + -
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Residues in contact with ILE 70 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58M TRP* 2.8 24.0 + - + +
59M VAL 3.9 4.5 - - - +
60M LYS* 3.7 32.5 - - + +
69M TRP* 1.3 77.8 - - - +
71M GLY* 1.3 56.4 + - - +
82M TYR* 3.5 5.4 - - + +
83M ASN* 2.7 34.5 + - - +
86M PHE* 4.0 38.0 - - + +
90M ALA* 4.0 11.0 - - + -
92M LEU* 5.7 2.0 - - + -
103M MET* 3.7 35.4 - - + -
116M TYR* 3.8 13.7 - - + -
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Residues in contact with GLY 71 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57M GLN* 3.4 2.1 - - - -
58M TRP* 2.8 29.8 + - - +
69M TRP* 3.5 18.0 + - - -
70M ILE* 1.3 83.5 - - - +
72M TYR* 1.3 59.9 + - - -
81M LYS 3.2 14.1 - - - -
82M TYR* 4.3 1.8 - - - -
92M LEU* 3.9 10.3 - - - -
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Residues in contact with TYR 72 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M THR* 3.9 24.0 - - + -
56M ILE 3.3 15.5 - - - +
57M GLN* 3.3 30.3 - - - +
69M TRP* 3.5 16.8 - + - -
71M GLY* 1.3 73.2 - - - -
73M ILE* 1.3 67.2 + - - +
74M TYR* 4.6 4.9 - - + -
79M GLY 4.4 10.1 - - - -
80M THR* 3.3 5.1 + - - -
81M LYS* 3.1 74.1 + - + +
92M LEU* 3.5 12.8 - - - +
254M TYR* 4.7 10.3 - + - -
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Residues in contact with ILE 73 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55M THR* 3.4 2.8 - - - -
56M ILE* 3.1 31.5 + - + +
72M TYR* 1.3 75.9 - - - +
74M TYR* 1.3 65.1 - - - +
75M PRO* 3.4 4.2 - - + +
78M ALA* 4.2 18.4 - - + +
79M GLY 3.4 4.9 - - - +
80M THR* 3.7 16.8 - - + -
92M LEU* 3.6 29.7 - - + +
93M THR* 3.7 19.5 - - - -
94M SER* 3.7 14.4 - - - +
101M VAL* 3.7 39.5 - - + -
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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