Contacts of the helix formed by residues 86 - 98 (chain B) in PDB entry 3MPZ
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 CYS 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A SER* 3.3 29.8 - - - +
50A LEU* 4.4 1.6 - - - -
53B CYS* 4.0 0.9 - - - -
55B GLU* 3.9 0.8 + - - -
84B MET 3.5 2.2 + - - -
85B PRO* 1.3 77.5 - - - +
87B GLY* 1.3 64.1 + - - +
88B ARG* 3.6 20.0 - - - -
89B CYS 3.1 5.1 + - - -
90B ARG* 2.8 25.7 + - - +
300B ZN 2.3 37.7 - - - -
91D GLN* 3.5 13.2 - - - +
120D PHE* 3.8 17.2 - - + +
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Residues in contact with GLY 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B CYS* 1.3 74.8 - - - +
88B ARG* 1.3 62.9 + - - +
90B ARG* 3.3 5.4 + - - +
91B GLN 3.1 11.6 + - - -
87D GLY* 3.1 36.6 - - - -
91D GLN* 2.9 19.5 + - - +
116D LEU* 4.0 19.7 - - - -
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Residues in contact with ARG 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A SER* 4.8 0.2 + - - -
49A GLY* 4.0 18.2 + - - -
50A LEU* 3.5 34.8 - - + +
51B GLY 3.4 23.4 + - - -
52B LEU* 4.3 2.8 - - - +
53B CYS* 3.3 26.5 - - - +
56B CYS* 3.6 30.7 - - - -
86B CYS* 3.3 5.4 - - - -
87B GLY* 1.3 75.7 - - - +
89B CYS* 1.3 65.9 + - - +
91B GLN* 3.2 5.0 + - - +
92B VAL* 3.0 37.0 + - + +
50C LEU* 4.0 27.5 + - + +
52C LEU* 5.3 5.9 - - - +
87D GLY 3.6 3.2 + - - -
88D ARG* 3.7 15.7 - - + +
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Residues in contact with CYS 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B CYS* 3.2 20.6 - - - -
55B GLU* 3.6 33.9 - - + +
56B CYS* 4.0 6.3 - - - -
85B PRO* 3.8 3.4 - - + -
86B CYS* 3.1 7.1 + - - +
88B ARG* 1.3 84.5 - - - +
90B ARG* 1.3 59.9 + - - +
92B VAL* 4.3 5.2 - - - +
93B LEU* 2.8 38.2 + - - +
300B ZN 2.3 36.1 - - - -
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Residues in contact with ARG 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B MET* 3.6 11.3 - - - +
85B PRO* 2.8 31.1 + - + +
86B CYS 2.8 15.2 + - - +
87B GLY 3.6 7.0 - - - +
88B ARG 3.2 0.2 - - - -
89B CYS* 1.3 74.7 - - - +
91B GLN* 1.3 62.7 + - - +
93B LEU* 4.7 2.2 - - - -
94B LEU* 3.1 23.4 + - - +
112B LEU* 3.7 26.1 - - + +
115B LEU* 2.8 54.8 + - + +
116B LEU* 3.9 14.5 - - + +
91D GLN* 5.9 0.2 - - - -
116D LEU* 3.6 26.9 - - - +
117D PRO 2.8 21.8 + - - -
118D ASP 3.1 25.3 + - - -
119D ALA* 3.7 8.5 - - - +
120D PHE 3.9 1.2 - - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B GLY 3.1 12.7 + - - +
88B ARG 3.2 8.5 + - - +
90B ARG* 1.3 75.8 - - - +
92B VAL* 1.3 65.6 + - - +
94B LEU* 3.4 25.6 + - - +
95B GLU* 3.6 3.3 + - - +
116B LEU* 3.7 14.7 - - - +
120B PHE* 3.1 30.3 + - - +
45C ASN* 3.5 16.1 + - - +
46C VAL* 3.8 17.1 - - - +
47C SER* 4.6 0.2 - - - -
50C LEU* 3.6 24.2 - - + -
86D CYS* 3.5 14.0 - - + -
87D GLY* 2.8 27.7 + - - +
90D ARG* 5.4 0.3 + - - -
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Residues in contact with VAL 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B GLU 5.4 0.9 - - - +
56B CYS* 4.7 9.2 - - - -
59B VAL* 4.1 31.2 - - + -
88B ARG* 3.0 32.2 + - - +
89B CYS* 3.2 6.5 + - - +
91B GLN* 1.3 74.9 - - - +
93B LEU* 1.3 64.5 + - + +
95B GLU* 3.2 7.3 + - - +
96B HIS* 3.1 28.0 - - + +
43C VAL* 5.7 1.1 - - + -
45C ASN* 3.6 11.2 - - + +
50C LEU* 4.0 33.0 - - + +
52C LEU* 4.6 12.1 - - + -
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Residues in contact with LEU 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B GLU* 4.3 15.7 - - + +
58B VAL* 5.1 0.2 - - + -
59B VAL* 3.9 15.3 - - + -
70B LEU* 3.5 28.7 - - + +
73B LEU* 3.7 25.1 - - + -
85B PRO* 4.0 26.5 - - + -
89B CYS* 2.8 27.3 + - - +
90B ARG* 3.9 4.5 - - - +
92B VAL* 1.3 74.2 - - + +
94B LEU* 1.3 57.0 + - - +
96B HIS 3.0 3.0 + - - +
97B GLY* 2.8 30.0 + - - -
98B GLY 3.9 0.2 + - - -
101B LEU* 3.8 12.4 - - + +
103B ILE* 4.3 12.8 - - + -
112B LEU* 3.9 6.3 - - + -
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Residues in contact with LEU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 4.6 0.9 + - - -
90B ARG 3.1 18.6 + - - +
91B GLN* 3.5 21.1 - - - +
92B VAL 3.2 0.4 - - - -
93B LEU* 1.3 75.5 - - - +
95B GLU* 1.3 58.9 + - - +
98B GLY* 3.0 25.8 + - - +
99B PRO* 3.5 40.2 - - + -
112B LEU* 3.5 14.6 - - + +
113B ARG* 5.7 1.6 - - - +
116B LEU* 4.3 7.2 - - + +
119B ALA* 3.4 33.2 - - + -
120B PHE 4.4 3.1 - - - +
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Residues in contact with GLU 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ARG* 3.1 16.1 + - - -
91B GLN 3.6 2.2 + - - +
92B VAL 3.2 12.2 + - - +
93B LEU 3.1 0.8 - - - -
94B LEU* 1.3 78.9 - - - +
96B HIS* 1.3 76.3 + - + +
18C TYR* 2.6 32.4 + - + +
21C TYR* 2.5 30.5 + - - -
44C GLU 4.4 0.4 - - - +
45C ASN* 3.3 17.1 + - - +
46C VAL* 2.9 32.9 + - - +
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Residues in contact with HIS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B VAL* 3.5 20.4 - - + +
62B LEU* 3.8 15.5 - - + -
63B HIS* 3.0 31.7 + - - -
68B GLY 5.4 0.4 - - - +
69B ARG* 3.4 21.6 + - - +
70B LEU* 2.9 32.8 + - + -
92B VAL* 3.1 27.7 + - + +
93B LEU 3.0 5.1 + - - +
95B GLU* 1.3 91.3 + - + +
97B GLY* 1.3 56.4 + - - +
18C TYR* 3.7 24.5 - + - -
43C VAL* 3.4 25.4 - - + +
44C GLU 4.3 3.0 + - - -
45C ASN* 5.3 0.2 + - - -
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Residues in contact with GLY 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 3.4 9.4 + - - -
70B LEU* 3.4 26.2 - - - +
93B LEU 2.8 9.9 + - - -
96B HIS* 1.3 76.0 - - - +
98B GLY* 1.3 68.4 + - - +
100B GLU* 3.6 14.4 - - - +
101B LEU* 3.6 20.7 + - - +
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Residues in contact with GLY 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B ARG* 3.2 12.8 - - - +
93B LEU 3.9 0.2 + - - -
94B LEU* 3.0 25.6 + - - -
97B GLY* 1.3 79.7 - - - +
99B PRO* 1.3 76.1 - - - +
100B GLU* 3.1 5.2 - - - -
101B LEU* 3.1 13.5 + - - +
112B LEU* 3.8 8.0 - - - +
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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