Contacts of the helix formed by residues 86 - 98 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91B GLN* 3.5 13.5 - - - +
120B PHE* 3.8 15.8 - - + +
47C SER* 3.3 30.3 - - - +
50C LEU* 4.3 1.6 - - - -
53D CYS* 4.0 0.7 - - - -
55D GLU* 3.9 0.2 + - - -
84D MET 3.4 2.0 + - - -
85D PRO* 1.3 76.1 - - - +
87D GLY* 1.3 63.8 + - - +
88D ARG* 3.6 20.0 - - - -
89D CYS 3.0 5.9 + - - -
90D ARG* 2.9 25.1 + - - +
300D ZN 2.4 37.8 - - - -
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Residues in contact with GLY 87 (chain D).
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 32.1 - - - -
91B GLN* 2.8 20.1 + - - -
116B LEU* 3.9 18.4 - - - -
86D CYS* 1.3 72.4 - - - +
88D ARG* 1.3 62.7 + - - +
90D ARG* 3.2 5.8 + - - +
91D GLN 3.1 17.5 + - - -
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Residues in contact with ARG 88 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU* 4.0 28.9 + - + +
52A LEU* 5.3 4.4 - - - +
87B GLY 3.6 2.8 + - - -
88B ARG* 3.7 17.0 - - + +
49C GLY* 4.0 16.4 + - - +
50C LEU* 3.4 36.1 - - + +
51D GLY 3.4 23.6 + - - -
52D LEU* 5.1 6.0 - - - +
53D CYS* 3.3 27.7 - - - +
56D CYS* 3.4 30.4 - - - -
86D CYS* 3.2 3.8 - - - -
87D GLY* 1.3 75.7 - - - +
89D CYS* 1.3 67.2 + - - +
91D GLN* 3.2 5.0 + - - +
92D VAL* 3.0 33.1 + - + +
300D ZN 4.0 0.4 - - - -
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Residues in contact with CYS 89 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D CYS* 3.3 19.7 - - - -
55D GLU* 3.7 32.8 - - + +
56D CYS* 4.0 7.2 - - - -
85D PRO* 4.1 3.6 - - + -
86D CYS* 3.0 7.1 + - - +
88D ARG* 1.3 84.3 - - - +
90D ARG* 1.3 61.0 + - - +
92D VAL* 3.9 4.9 - - - +
93D LEU* 2.8 37.5 + - - +
300D ZN 2.3 35.7 - - - -
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Residues in contact with ARG 90 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B GLN* 5.4 0.2 + - - -
116B LEU* 3.6 26.2 - - - +
117B PRO 2.8 21.6 + - - -
118B ASP* 3.2 24.9 + - - +
119B ALA* 3.5 10.3 - - - +
120B PHE 3.7 2.8 - - - +
84D MET* 4.0 8.5 - - - +
85D PRO* 2.9 32.1 + - + +
86D CYS* 2.9 15.8 + - - +
87D GLY 3.6 6.5 - - - +
88D ARG 3.2 0.4 - - - -
89D CYS* 1.3 77.6 - - - +
91D GLN* 1.3 57.1 + - - +
93D LEU* 4.6 2.0 - - - -
94D LEU* 3.0 28.6 + - - +
112D LEU* 3.7 26.2 - - + +
115D LEU* 2.8 55.7 + - + +
116D LEU* 3.8 15.2 - - + +
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Residues in contact with GLN 91 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A ASN* 3.5 21.2 + - - +
46A VAL* 3.7 18.1 - - - +
50A LEU* 3.7 16.6 - - + -
86B CYS* 3.5 14.3 - - + -
87B GLY* 2.9 28.8 + - - +
90B ARG* 5.8 0.3 + - - -
87D GLY 3.1 11.5 + - - +
88D ARG 3.5 7.6 - - - +
90D ARG* 1.3 75.6 - - - +
92D VAL* 1.3 65.8 + - - +
94D LEU* 3.3 23.2 + - - +
95D GLU* 3.4 7.8 + - - +
116D LEU* 3.8 13.9 - - - +
120D PHE* 3.2 29.7 + - - +
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Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A VAL* 5.8 0.9 - - + -
45A ASN* 3.5 11.0 - - + +
50A LEU* 4.0 34.3 - - + +
52A LEU* 4.8 10.1 - - + -
55D GLU 5.3 0.7 - - - +
56D CYS* 4.8 10.8 - - - +
59D VAL* 3.9 31.9 - - + -
88D ARG* 3.0 32.4 + - - +
89D CYS* 3.9 6.3 - - - +
91D GLN* 1.3 74.7 - - - +
93D LEU* 1.3 63.5 + - + +
95D GLU* 3.1 7.6 + - - +
96D HIS* 3.1 26.8 - - + +
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Residues in contact with LEU 93 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D GLU* 4.2 19.5 - - + +
58D VAL* 5.1 0.2 - - + -
59D VAL* 3.9 16.6 - - + -
70D LEU* 3.7 26.4 - - + +
73D LEU* 3.7 26.7 - - + -
85D PRO* 4.2 20.0 - - + -
89D CYS 2.8 32.6 + - - +
90D ARG* 3.9 4.5 - - - +
92D VAL* 1.3 70.6 - - + +
94D LEU* 1.3 65.9 + - - +
96D HIS 2.9 3.5 + - - -
97D GLY* 2.9 23.0 + - - -
101D LEU* 3.9 12.4 - - + +
103D ILE* 4.3 13.5 - - + -
112D LEU* 3.8 6.7 - - + -
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Residues in contact with LEU 94 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 4.8 0.5 + - - -
90D ARG 3.0 18.3 + - - +
91D GLN* 3.5 17.5 - - - +
92D VAL 3.3 0.4 - - - -
93D LEU* 1.3 75.5 - - - +
95D GLU* 1.3 60.2 + - - +
98D GLY* 2.9 54.6 + - - +
99D PRO* 3.5 15.3 - - + -
112D LEU* 3.4 15.2 - - + +
113D ARG* 5.5 2.5 - - - +
116D LEU* 4.2 10.3 - - + +
119D ALA* 3.4 33.0 - - + -
120D PHE 4.6 3.1 - - - +
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Residues in contact with GLU 95 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 2.7 34.6 + - + +
21A TYR* 2.6 30.2 + - - -
44A GLU 4.3 0.4 - - - +
45A ASN* 3.3 17.8 + - - +
46A VAL* 3.0 33.5 + - - +
69D ARG* 3.2 14.7 + - - -
91D GLN* 3.4 2.5 + - - +
92D VAL 3.1 13.8 + - - +
93D LEU 3.1 0.6 - - - -
94D LEU* 1.3 80.6 - - - +
96D HIS* 1.3 72.7 + - - +
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Residues in contact with HIS 96 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.6 25.6 - + - -
43A VAL* 3.5 24.7 - - + +
44A GLU 4.3 2.0 + - - -
45A ASN* 5.3 0.6 + - - -
59D VAL* 3.4 20.3 - - + +
62D LEU* 3.7 16.4 - - + -
63D HIS* 3.0 32.2 + - - -
68D GLY 4.3 1.7 + - - +
69D ARG* 3.4 21.1 + - - +
70D LEU* 3.0 32.0 + - + -
92D VAL* 3.1 27.8 - - + +
93D LEU 2.9 4.5 + - - +
95D GLU* 1.3 88.9 + - + +
97D GLY* 1.3 58.0 + - - +
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Residues in contact with GLY 97 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 3.3 12.9 + - - -
70D LEU* 3.5 24.9 - - - +
93D LEU 2.9 10.3 + - - -
96D HIS* 1.3 77.5 - - - +
98D GLY* 1.3 69.6 + - - +
100D GLU* 4.4 2.1 + - - +
101D LEU* 3.7 18.9 + - - +
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Residues in contact with GLY 98 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69D ARG* 3.3 12.3 - - - +
93D LEU 4.1 0.2 + - - -
94D LEU* 2.9 30.6 + - - +
97D GLY* 1.3 81.8 - - - +
99D PRO* 1.3 76.3 - - - +
100D GLU 3.2 3.1 + - - -
101D LEU* 3.2 11.4 + - - +
112D LEU* 3.8 5.5 - - - +
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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