Contacts of the helix formed by residues 72 - 81 (chain M) in PDB entry 5KZ5
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 72 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77L ASN* 3.2 31.5 - - - +
78L LEU 3.7 16.2 - - - +
79L ARG* 3.8 9.8 - - + +
80L LYS* 3.2 23.7 - - - +
81L SER 3.1 28.8 + - - +
83L THR* 3.5 23.9 + - + +
70M ASP* 3.2 25.4 - - - +
71M PRO* 1.3 78.3 - - + +
73M VAL* 1.3 58.1 + - - +
75M ASP* 2.7 29.4 - - - +
76M ALA* 4.0 1.9 + - - +
83l GLY 4.4 5.1 + - - -
84l LYS* 3.6 31.3 - - - +
111l GLY 4.9 0.9 - - - -
113l THR* 3.6 29.6 - - + +
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Residues in contact with VAL 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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45K ASP* 3.3 33.4 - - + +
47K ASP* 5.4 1.3 - - - +
48K ALA* 3.7 26.5 - - + -
49K THR* 3.4 23.3 - - - +
80L LYS 5.9 2.2 - - - +
81L SER 6.4 0.7 - - - +
70M ASP* 3.7 23.1 + - + +
72M ARG* 1.3 75.9 - - - +
74M LEU* 1.4 67.6 + - + +
76M ALA* 3.1 23.3 + - - +
77M MET* 3.4 8.7 + - + +
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Residues in contact with LEU 74 (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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48K ALA* 4.0 13.2 - - + -
49K THR* 4.7 2.9 - - - +
205L TYR 4.7 2.4 - - - +
207L GLY* 3.4 23.3 - - - -
208L LYS* 3.8 16.8 - - - +
209L ASP 3.3 29.2 - - - +
210L ALA* 4.0 13.9 - - + +
70M ASP 3.9 8.5 - - - +
71M PRO 3.4 2.5 + - - +
73M VAL* 1.4 93.5 - - + +
75M ASP* 1.4 60.2 + - - +
76M ALA 3.3 0.2 - - - -
77M MET* 3.3 44.0 + - + +
78M LEU* 3.8 4.2 + - - -
81M LEU* 4.5 14.9 - - + +
261M GLY* 6.2 0.7 - - - -
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Residues in contact with ASP 75 (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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83L THR* 3.0 29.0 - - - +
84L LEU 3.3 6.4 - - - +
85L GLY* 3.1 16.1 + - - +
86L HIS* 3.1 19.8 + - - -
87L PRO* 3.6 32.3 - - + -
88L GLY* 3.7 12.0 - - - +
89L SER* 3.5 9.5 + - - -
205L TYR 5.1 2.9 - - - -
207L GLY* 5.0 1.5 - - - +
71M PRO 2.9 17.0 + - - +
72M ARG* 2.7 21.0 - - - +
74M LEU* 1.4 72.3 - - - +
76M ALA* 1.3 59.4 + - - +
77M MET 3.2 6.5 + - - -
78M LEU* 3.7 7.4 + - - +
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Residues in contact with ALA 76 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54K ARG* 3.0 38.3 + - - +
81L SER* 6.1 2.9 - - - -
83L THR 4.0 12.1 - - - +
84L LEU* 3.3 22.7 - - + +
89L SER* 4.2 3.6 - - - -
72M ARG 4.3 2.2 - - - +
73M VAL* 3.1 12.8 + - - +
75M ASP* 1.3 76.9 + - - +
77M MET* 1.4 56.9 + - - +
78M LEU 3.5 1.3 - - - -
79M PRO* 4.4 3.7 - - - +
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Residues in contact with MET 77 (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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49K THR* 3.6 42.2 - - + +
54K ARG* 4.7 9.0 - - - +
210L ALA* 6.5 0.7 - - - -
73M VAL* 3.8 6.3 - - + +
74M LEU* 3.3 37.0 - - + +
75M ASP 3.2 0.4 - - - -
76M ALA* 1.4 78.2 - - - +
78M LEU* 1.4 62.9 + - - +
79M PRO* 3.4 3.4 - - - -
80M TYR* 3.2 19.6 + - + +
81M LEU* 3.0 41.4 + - + +
85M TYR* 3.9 34.3 - - + +
302M VAL* 4.8 3.8 - - + -
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Residues in contact with LEU 78 (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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87L PRO 4.5 1.3 - - - +
88L GLY* 3.6 9.9 - - - -
89L SER 3.6 22.9 - - - +
90L LEU 3.6 16.4 - - - +
91L ASP* 4.1 13.7 - - + -
171L LYS* 5.4 3.8 - - - -
204L ALA 3.2 27.1 - - - +
205L TYR* 3.7 34.3 - - + +
74M LEU 3.8 3.9 + - - +
75M ASP* 3.7 14.6 + - - +
76M ALA 3.5 0.4 - - - -
77M MET* 1.4 74.5 - - - +
79M PRO* 1.3 70.8 - - + +
81M LEU* 3.1 16.2 + - + +
82M ILE* 3.3 18.3 + - + +
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Residues in contact with PRO 79 (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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54K ARG* 4.1 13.9 - - - +
89L SER* 4.2 13.5 - - - -
90L LEU* 4.0 36.1 - - + +
76M ALA 4.4 4.0 - - - +
77M MET 3.5 4.7 - - - -
78M LEU* 1.3 93.3 - - + +
80M TYR* 1.4 64.0 + - + +
82M ILE* 3.3 8.8 - - + +
83M ASN* 3.0 30.6 + - - +
66k ALA* 4.0 17.9 - - + -
67k PRO* 5.8 2.0 - - + +
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Residues in contact with TYR 80 (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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49K THR* 5.4 4.7 - - + -
51K THR* 3.5 42.2 - - + +
53K ARG* 4.9 1.0 - - - -
54K ARG* 3.9 24.5 - - - -
77M MET* 3.2 21.9 + - + +
79M PRO* 1.4 79.1 - - + +
81M LEU* 1.4 60.1 + - - +
83M ASN* 5.0 0.2 - - - -
84M TYR* 3.0 75.6 + + + +
85M TYR* 3.7 2.0 - - - -
451Q SER 4.6 6.5 - - - -
452Q ILE* 3.6 29.6 - - + +
67k PRO* 3.8 31.0 - - + +
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Residues in contact with LEU 81 (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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109L PHE* 5.4 6.0 - - + -
203L LEU 3.7 14.8 - - - +
204L ALA* 3.6 36.7 - - - +
205L TYR 4.0 11.9 - - - +
206L SER 4.8 3.4 - - - +
74M LEU* 4.5 15.9 - - + +
77M MET* 3.0 31.6 + - + +
78M LEU* 3.1 17.6 + - + +
80M TYR* 1.4 75.3 - - - +
82M ILE* 1.3 58.6 + - - +
85M TYR* 3.3 43.5 - - + +
299M PRO* 6.1 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