Contacts of the helix formed by residues 86 - 98 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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53A CYS* 3.9 0.9 - - - -
55A GLU* 3.9 0.2 + - - -
84A MET 3.6 2.0 + - - -
85A PRO* 1.3 76.1 - - - +
87A GLY* 1.3 68.3 + - - +
88A ARG* 3.6 20.0 - - - -
89A CYS* 3.1 5.9 + - - +
90A ARG* 2.9 19.9 + - - +
300A ZN 2.3 38.5 - - - -
47B SER* 3.3 30.5 - - - +
50B LEU* 4.3 2.0 - - - -
91C GLN* 3.4 14.1 - - - +
120C PHE* 4.0 13.1 - - + +
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Residues in contact with GLY 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A CYS* 1.3 73.4 - - - +
88A ARG* 1.3 62.0 + - - +
90A ARG* 3.2 5.6 + - - +
91A GLN 3.1 16.3 + - - -
87C GLY* 3.1 33.0 - - - -
91C GLN* 2.8 20.7 + - - +
116C LEU* 4.0 19.2 - - - +
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Residues in contact with ARG 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A GLY 3.2 25.5 + - - -
52A LEU* 4.1 2.4 - - - +
53A CYS* 3.5 34.6 - - - +
56A CYS* 3.4 30.4 - - - -
86A CYS* 3.3 4.5 - - - -
87A GLY* 1.3 74.1 - - - +
89A CYS* 1.3 59.9 + - - +
91A GLN* 3.2 5.0 + - - +
92A VAL* 2.9 34.2 + - + +
47B SER* 4.9 0.2 + - - -
49B GLY* 4.1 16.0 + - - -
50B LEU* 3.5 35.7 - - + +
87C GLY 3.5 3.0 + - - -
88C ARG* 3.7 16.8 - - + +
50D LEU* 4.1 28.5 + - + +
52D LEU* 5.1 8.1 - - - +
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Residues in contact with CYS 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A CYS* 3.2 20.4 - - - -
55A GLU* 3.5 34.5 - - + +
56A CYS* 4.1 5.6 - - - -
85A PRO* 4.1 3.8 - - + -
86A CYS* 3.1 7.5 + - - +
88A ARG* 1.3 85.5 - - - +
90A ARG* 1.3 60.8 + - - +
92A VAL* 4.3 4.5 - - - +
93A LEU* 2.7 39.1 + - - +
300A ZN 2.3 35.2 - - - -
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Residues in contact with ARG 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A MET* 3.6 15.0 - - - +
85A PRO* 2.8 35.1 + - + +
86A CYS 2.9 13.7 + - - +
87A GLY* 3.2 7.4 + - - +
89A CYS* 1.3 75.4 - - - +
91A GLN* 1.3 56.3 + - - +
93A LEU* 4.6 2.5 - - - -
94A LEU* 3.0 29.3 + - - +
112A LEU* 3.6 26.9 - - + +
115A LEU* 2.8 50.7 + - + +
116A LEU* 3.9 14.6 - - + +
91C GLN* 6.0 0.2 - - - -
116C LEU* 3.7 24.7 - - - +
117C PRO 2.8 22.2 + - - -
118C ASP 3.0 26.7 + - - -
119C ALA* 3.8 6.3 - - - +
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A GLY 3.1 6.7 + - - +
88A ARG 3.5 7.4 - - - +
90A ARG* 1.3 73.9 - - - +
92A VAL* 1.3 66.3 + - - +
94A LEU* 3.3 25.1 + - - +
95A GLU* 3.5 4.3 + - - +
116A LEU* 3.8 14.3 - - - +
119A ALA* 5.2 0.2 - - - -
120A PHE* 2.9 31.7 + - - +
86C CYS* 3.4 14.7 - - + -
87C GLY* 2.8 35.1 + - - +
90C ARG* 5.9 0.2 + - - -
45D ASN* 3.5 14.1 + - - +
46D VAL* 3.7 16.1 - - - +
47D SER* 4.6 0.2 - - - -
50D LEU* 3.6 24.7 - - + -
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Residues in contact with VAL 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU 5.3 1.1 - - - +
56A CYS* 4.9 9.2 - - - -
59A VAL* 3.9 31.9 - - + -
88A ARG* 2.9 31.7 + - - +
89A CYS* 3.2 6.5 + - - +
91A GLN* 1.3 77.3 - - - +
93A LEU* 1.3 61.0 + - + +
95A GLU* 3.1 7.6 + - - +
96A HIS* 3.0 29.0 - - + +
43D VAL* 5.7 1.3 - - + -
45D ASN* 3.5 11.2 - - + +
50D LEU* 4.1 32.8 - - + +
52D LEU* 4.6 11.7 - - + -
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Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A GLU* 4.3 17.0 - - + +
58A VAL* 5.1 0.2 - - + -
59A VAL* 3.8 16.4 - - + -
70A LEU* 3.7 21.0 - - + +
73A LEU* 3.6 33.7 - - + -
85A PRO* 4.4 13.0 - - + -
89A CYS 2.7 33.1 + - - +
90A ARG* 3.9 5.6 - - - +
92A VAL* 1.3 71.8 - - + +
94A LEU* 1.3 62.7 + - - +
96A HIS* 3.0 3.5 + - - +
97A GLY* 2.9 23.0 + - - -
101A LEU* 3.8 13.1 - - + +
103A ILE* 4.3 19.3 - - + -
112A LEU* 3.9 6.1 - - + -
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Residues in contact with LEU 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 4.8 0.5 + - - -
90A ARG 3.0 18.3 + - - +
91A GLN* 3.5 19.5 - - - +
92A VAL 3.2 0.4 - - - -
93A LEU* 1.3 75.7 - - - +
95A GLU* 1.3 59.9 + - - +
98A GLY* 2.9 54.0 + - - +
99A PRO* 3.6 13.9 - - + -
112A LEU* 3.4 15.7 - - + +
113A ARG* 5.6 2.0 - - - +
116A LEU* 4.2 6.1 - - + +
119A ALA* 3.3 35.2 - - + -
120A PHE 4.4 3.1 - - - +
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Residues in contact with GLU 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.1 15.1 + - - -
91A GLN* 3.5 2.3 + - - +
92A VAL 3.1 14.1 + - - +
94A LEU* 1.3 79.7 - - - +
96A HIS* 1.3 67.8 + - + +
18D TYR* 2.7 43.4 + - + +
21D TYR* 2.6 26.6 + - - -
44D GLU 4.6 0.2 - - - +
45D ASN* 3.2 16.8 + - - +
46D VAL* 3.0 33.2 + - - +
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Residues in contact with HIS 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A VAL* 3.4 20.8 - - + +
62A LEU* 3.8 15.9 - - + -
63A HIS* 3.0 29.8 + - - -
68A GLY 4.4 0.9 - - - +
69A ARG* 3.4 22.1 + - - +
70A LEU* 2.9 32.9 + - + -
92A VAL* 3.0 28.7 + - + +
93A LEU 3.0 5.2 + - - +
95A GLU* 1.3 91.4 + - + +
97A GLY* 1.3 56.7 - - - +
18D TYR* 3.6 24.9 - + - -
43D VAL* 3.5 26.4 - - + +
44D GLU 4.4 2.8 + - - -
45D ASN* 5.2 0.6 + - - -
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Residues in contact with GLY 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.3 13.5 + - - -
70A LEU* 3.5 24.1 - - - +
93A LEU 2.9 10.3 + - - -
96A HIS* 1.3 79.3 - - - +
98A GLY* 1.3 63.8 + - - +
100A GLU* 4.4 2.4 + - - +
101A LEU* 3.7 19.1 + - - +
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Residues in contact with GLY 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A ARG* 3.3 12.6 - - - +
94A LEU* 2.9 31.3 + - - +
97A GLY* 1.3 79.3 - - - +
99A PRO* 1.3 76.3 - - - +
100A GLU 3.2 3.0 + - - -
101A LEU* 3.2 13.0 + - - +
112A LEU* 3.9 5.0 - - - +
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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