Contacts of the strand formed by residues 81 - 86 (chain M) in PDB entry 7K63
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 PHE 81 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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56M GLN* 3.5 15.9 - - - -
66M LEU* 4.0 22.0 - - + -
67M ILE* 4.3 11.0 - - + -
73M LEU* 3.1 33.6 - - + +
77M VAL* 3.6 22.4 - - + -
78M PRO* 3.4 11.4 + - + -
79M SER 3.3 7.7 - - - +
80M ARG* 1.3 97.6 - - - +
82M SER* 1.3 60.9 + - - +
92M LEU* 4.9 5.4 - - + -
93M THR 3.3 3.4 - - - -
94M ILE* 3.5 38.6 - - + -
101M ASP* 3.3 21.5 - - - -
105M TYR* 3.8 13.9 - + - -
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Residues in contact with SER 82 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67M ILE* 3.4 9.2 - - - +
71M THR 5.5 0.2 - - - -
73M LEU* 4.8 6.1 - - - -
79M SER 4.9 3.6 - - - -
80M ARG 4.5 2.2 - - - -
81M PHE* 1.3 76.9 - - - +
83M GLY* 1.3 58.7 + - - +
92M LEU* 3.5 1.4 - - - +
93M THR* 2.6 59.8 + - - +
95M ASN* 4.3 7.0 + - - -
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Residues in contact with GLY 83 (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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54M TRP* 5.5 0.2 - - - -
67M ILE* 3.3 14.1 - - - +
70M ALA 3.4 15.3 - - - -
71M THR* 3.4 20.1 + - - +
82M SER* 1.3 76.5 - - - +
84M SER* 1.3 63.5 + - - -
91M SER* 3.2 14.4 - - - -
93M THR* 5.4 0.7 - - - -
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Residues in contact with SER 84 (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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54M TRP* 5.8 0.3 + - - -
70M ALA 3.6 9.8 - - - +
71M THR* 4.1 7.6 - - - -
83M GLY* 1.3 75.4 - - - -
85M GLY* 1.3 70.4 + - - +
90M PHE* 3.8 6.8 - - - +
91M SER* 2.7 41.0 + - - +
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Residues in contact with GLY 85 (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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70M ALA* 4.0 6.1 - - - +
71M THR* 5.0 3.1 - - - +
84M SER* 1.3 87.9 + - - +
86M SER* 1.3 70.1 + - - -
89M ASP* 3.2 24.2 - - - -
90M PHE* 3.7 10.1 - - - -
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Residues in contact with SER 86 (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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50M SER* 4.0 19.3 + - - +
71M THR* 6.0 0.2 - - - +
85M GLY* 1.3 79.3 + - - -
87M GLY* 1.3 61.6 + - - +
88M GLN 3.0 7.6 + - - -
89M ASP* 3.0 19.6 + - - +
90M PHE* 3.8 9.9 - - - -
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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