Contacts of the helix formed by residues 89 - 100 (chain K) in PDB entry 6MZL
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 THR 89 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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935E GLU* 3.8 29.6 - - + -
937E ALA* 4.9 12.1 - - + -
87K GLN* 3.6 16.8 - - + +
88K PRO* 1.3 68.0 - - - +
90K LEU* 1.3 66.7 + - - +
91K SER* 4.0 4.7 + - - -
92K ASP* 2.4 47.1 + - - +
93K ILE* 3.2 21.8 - - - +
151O ILE* 4.5 7.0 - - - -
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Residues in contact with LEU 90 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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934E TYR* 4.2 24.5 - - + -
89K THR* 1.3 79.0 - - - +
91K SER* 1.3 59.2 + - - +
93K ILE* 2.9 11.2 + - - +
94K VAL* 2.9 29.4 + - - +
120O LEU* 4.2 40.8 - - + +
121O MET* 5.2 4.7 - - + -
123O LEU* 4.0 20.0 - - + -
148O ASP* 5.3 3.1 - - - +
150O ARG* 4.8 9.9 - - + +
151O ILE* 3.7 29.4 - - + +
154O LEU* 4.9 7.7 - - + +
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Residues in contact with SER 91 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89K THR* 3.5 3.6 + - - -
90K LEU* 1.3 75.8 - - - +
92K ASP* 1.3 63.6 + - - +
94K VAL* 3.3 12.6 - - - +
95K VAL* 2.9 38.0 + - - +
120O LEU* 5.0 8.7 - - - +
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Residues in contact with ASP 92 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79K TYR* 4.6 10.3 - - + -
80K CYS* 3.6 26.0 - - - -
87K GLN 3.9 1.7 - - - +
88K PRO* 3.3 7.3 - - - +
89K THR* 2.4 46.1 + - - +
91K SER* 1.3 79.2 - - - +
93K ILE* 1.3 55.8 + - + +
95K VAL* 3.3 5.8 + - - +
96K THR* 2.6 36.0 + - - -
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Residues in contact with ILE 93 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K ILE* 4.9 6.5 - - + -
76K ALA* 3.7 29.2 - - + -
88K PRO* 4.2 14.8 - - + +
89K THR 3.2 15.9 - - - +
90K LEU* 2.9 6.4 + - - +
92K ASP* 1.3 78.1 - - + +
94K VAL* 1.3 60.2 + - - +
96K THR* 3.6 6.3 - - - +
97K LEU* 2.8 40.5 + - + +
144O PHE* 4.8 4.0 - - + -
151O ILE* 3.9 19.5 - - + -
154O LEU* 4.4 17.0 - - + -
155O ILE* 4.2 26.2 - - + -
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Residues in contact with VAL 94 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90K LEU 2.9 20.4 + - - +
91K SER* 3.3 16.6 - - - +
92K ASP 3.2 0.4 - - - -
93K ILE* 1.3 76.6 - - - +
95K VAL* 1.3 62.6 + - + +
97K LEU* 3.2 5.4 + - - +
98K VAL* 2.9 44.3 + - + +
104K VAL* 4.9 19.5 - - + +
116O LEU* 5.2 10.3 - - + -
120O LEU* 4.5 24.2 - - + -
154O LEU* 5.2 6.7 - - + -
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Residues in contact with VAL 95 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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922E GLN* 5.0 13.5 - - + +
79K TYR* 3.3 32.8 - - + +
91K SER* 2.9 19.0 + - - +
92K ASP* 3.8 4.7 - - - +
94K VAL* 1.3 80.2 - - + +
96K THR* 1.3 56.8 + - - +
98K VAL* 4.1 5.7 - - - +
99K GLU* 2.8 34.7 + - + +
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Residues in contact with THR 96 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72K ILE* 4.4 11.0 - - + +
75K SER* 3.7 30.1 - - - -
76K ALA* 4.3 12.1 - - + +
79K TYR* 4.5 14.7 - - + -
92K ASP 2.6 22.8 + - - -
93K ILE* 3.4 18.8 - - + +
95K VAL* 1.3 77.9 - - - +
97K LEU* 1.3 52.9 + - + +
99K GLU* 3.2 6.6 + - + +
100K MET* 2.5 50.4 + - + +
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Residues in contact with LEU 97 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K TYR* 4.0 20.2 - - - +
72K ILE* 4.4 26.7 - - + -
93K ILE* 2.8 34.5 + - + +
94K VAL* 4.0 3.4 - - - +
96K THR* 1.3 73.7 - - + +
98K VAL* 1.3 61.4 + - - +
100K MET* 3.1 6.9 - - + +
101K GLY 2.8 22.7 + - - -
102K PHE* 2.9 30.5 + - + +
104K VAL* 4.6 12.3 - - + -
107K LEU* 5.2 3.1 - - + -
154O LEU* 4.9 14.1 - - + -
155O ILE* 5.8 2.2 - - + -
158O ALA* 4.1 25.1 - - + -
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Residues in contact with VAL 98 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K VAL* 2.9 27.3 + - + +
95K VAL* 4.1 5.4 - - - +
97K LEU* 1.3 74.8 - - - +
99K GLU* 1.3 64.2 + - - +
101K GLY* 3.1 12.0 + - - -
102K PHE 3.8 19.5 - - - +
104K VAL* 4.4 13.9 - - + -
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Residues in contact with GLU 99 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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916E LYS* 3.5 22.3 + - - -
919E GLU* 3.1 29.2 - - - +
75K SER* 6.3 2.0 - - - -
79K TYR* 6.0 7.2 - - + -
95K VAL* 2.8 24.7 + - + +
96K THR* 3.2 8.7 - - + +
98K VAL* 1.3 77.6 - - - +
100K MET* 1.3 60.2 + - + +
101K GLY* 3.3 3.1 + - - -
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Residues in contact with MET 100 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68K TYR* 3.6 41.2 + - + +
71K GLU* 3.7 21.3 - - + +
72K ILE* 3.6 39.3 - - + +
75K SER* 3.6 22.4 - - - +
96K THR* 2.5 31.6 + - + +
97K LEU* 3.1 11.8 + - - +
99K GLU* 1.3 77.8 - - + +
101K GLY* 1.3 62.7 + - - +
206O GLU* 5.0 7.4 - - - +
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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