Contacts of the strand formed by residues 113 - 119 (chain M) in PDB entry 5D4D
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 113 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95M TYR* 3.4 6.1 - - - -
96M ALA* 2.7 57.8 + - + +
111M ASP* 4.5 8.5 - - - +
112M GLU* 1.3 76.5 - - - +
114M PHE* 1.3 64.4 + - - +
115M LEU* 3.6 12.5 + - + +
369M PRO* 4.2 14.8 - - + +
370M ALA* 3.7 37.0 - - + +
373M VAL* 4.8 14.8 - - + -
280P GLN* 4.3 14.1 - - + +
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Residues in contact with PHE 114 (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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93M PRO* 3.5 26.5 - - + -
94M LEU 3.9 2.9 - - - -
95M TYR* 3.3 29.1 - + + -
112M GLU 4.2 0.6 + - - -
113M VAL* 1.3 73.5 - - - +
115M LEU* 1.3 63.8 + - - +
116M GLY* 3.7 20.0 + - - -
117M HIS* 3.2 21.1 - + - -
373M VAL* 5.9 0.7 - - - +
375M SER* 3.8 10.2 + - - -
279P GLN* 3.4 42.4 + - + +
280P GLN* 3.5 33.1 + - - +
283P GLY* 3.1 34.8 - - - -
284P ARG* 3.6 3.1 - - - -
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Residues in contact with LEU 115 (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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48M PHE* 3.4 36.6 - - + -
94M LEU* 2.8 36.2 + - + +
96M ALA* 3.6 16.8 - - + -
113M VAL* 4.0 14.1 - - + +
114M PHE* 1.3 76.0 - - - +
116M GLY* 1.3 57.8 + - - +
348M LEU* 5.3 0.9 - - + -
351M LEU* 5.0 8.3 - - + -
373M VAL* 4.1 25.6 - - + -
375M SER* 3.4 21.2 - - - +
378M LEU* 4.3 16.2 - - + +
379M GLU* 3.3 17.5 + - - +
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Residues in contact with GLY 116 (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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94M LEU* 2.9 26.4 + - - +
114M PHE* 3.4 26.1 + - - -
115M LEU* 1.3 80.7 - - - +
117M HIS* 1.3 66.2 + - - -
379M GLU* 3.6 21.8 - - - -
279P GLN* 4.0 1.2 - - - +
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Residues in contact with HIS 117 (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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77M PRO* 4.7 13.2 - - + +
91M GLN* 3.2 43.4 + - + +
92M ALA 3.3 7.2 - - - +
93M PRO* 3.4 28.1 - - + +
94M LEU* 5.2 0.4 - - - -
114M PHE* 3.2 25.9 - + - -
116M GLY* 1.3 78.1 - - - -
118M ILE* 1.3 61.3 + - - +
119M PRO* 3.3 11.1 - - - +
379M GLU* 4.5 10.6 + - - +
382M ILE* 4.6 5.7 - - - +
283P GLY 3.7 11.9 + - - -
284P ARG* 4.2 10.6 - - + +
285P GLU* 4.7 12.2 + - + +
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Residues in contact with ILE 118 (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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26M TYR* 3.3 24.7 - - - +
30M LEU* 3.6 26.7 - - + -
44M ILE* 3.6 20.4 - - + -
73M LEU* 4.3 11.2 - - + -
91M GLN* 3.9 2.0 - - - -
92M ALA* 2.9 38.6 + - - +
94M LEU* 4.0 14.5 - - + +
116M GLY 4.3 0.6 + - - -
117M HIS* 1.3 72.5 - - - +
119M PRO* 1.3 69.0 - - + +
120M LEU* 3.5 0.7 + - - +
340M MET* 4.9 7.9 - - - -
344M PHE* 3.6 34.8 - - + -
382M ILE* 5.3 5.4 - - + -
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Residues in contact with PRO 119 (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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26M TYR* 2.4 32.4 + - - -
89M THR* 4.3 14.4 - - + -
90M TYR 3.7 6.7 - - - +
91M GLN* 3.9 6.3 - - + +
117M HIS 3.3 10.5 - - - +
118M ILE* 1.3 87.5 - - + +
120M LEU* 1.3 59.7 + - - +
127M PHE* 4.4 1.8 - - + -
129M ILE* 4.2 12.1 - - + -
382M ILE* 3.5 19.3 - - + +
383M ARG* 5.9 1.8 - - - -
386M PHE* 3.9 41.1 - - + -
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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