Contacts of the helix formed by residues 93 - 108 (chain B) in PDB entry 4MCA
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 GLY 93 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B VAL* 5.2 1.2 - - - +
92B GLY* 1.3 74.1 - - - -
94B GLY* 1.3 66.8 + - - -
95B LYS 3.4 2.2 - - - -
96B THR* 3.1 9.3 + - - -
97B LEU* 3.1 21.4 + - - +
116B THR* 3.9 1.4 + - - -
117B ILE* 4.2 23.8 - - - -
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Residues in contact with GLY 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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93B GLY* 1.3 71.5 - - - -
95B LYS* 1.3 57.5 + - - +
97B LEU* 3.1 10.9 + - - +
98B ASP* 2.8 39.3 + - - -
117B ILE* 4.9 4.4 - - - +
120B THR* 6.1 0.7 - - - -
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Residues in contact with LYS 95 (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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64B PHE* 4.6 4.9 - - + -
66B GLY* 4.4 28.7 + - - +
93B GLY 3.3 0.8 + - - -
94B GLY* 1.3 74.0 - - - +
96B THR* 1.3 60.8 + - - +
98B ASP* 3.5 9.2 + - - +
99B THR* 2.8 30.3 + - - +
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Residues in contact with THR 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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35B ILE* 3.5 31.3 - - + +
36B ALA* 4.4 1.3 - - - -
37B ASP* 4.7 8.8 + - - +
40B VAL* 6.2 0.2 - - - +
64B PHE* 3.2 25.9 - - + -
90B GLY* 4.4 0.9 - - - -
91B VAL 3.4 32.9 + - - +
92B GLY* 4.8 0.5 - - - -
93B GLY 3.1 15.2 + - - -
95B LYS* 1.3 74.7 - - - +
97B LEU* 1.3 62.2 + - - +
99B THR* 3.1 3.8 + - - -
100B ALA* 2.8 26.9 + - - +
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Residues in contact with LEU 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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90B GLY 3.8 26.9 - - - +
92B GLY 3.8 20.2 - - - +
93B GLY 3.1 15.8 + - - +
94B GLY* 3.1 8.5 + - - +
96B THR* 1.3 75.5 - - - +
98B ASP* 1.3 60.4 + - - +
100B ALA* 3.2 3.8 + - - +
101B LYS* 3.0 34.0 + - - +
113B LEU* 3.9 21.3 - - + +
114B ILE 4.0 15.5 - - - +
115B PRO* 3.9 24.2 - - + -
123B PRO* 4.2 19.1 - - + -
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Residues in contact with ASP 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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73B ILE* 6.0 0.2 - - - -
94B GLY* 2.8 24.0 + - - +
95B LYS* 3.7 8.2 - - - +
97B LEU* 1.3 76.6 - - - +
99B THR* 1.3 63.9 + - - +
101B LYS* 3.5 13.3 + - - +
102B ALA* 3.1 22.9 + - - +
122B ALA* 5.2 7.7 - - - +
127B LEU 4.5 1.6 - - - +
128B SER* 3.0 36.5 + - - +
129B VAL 4.8 8.3 + - - +
143B TYR* 4.4 0.7 + - - -
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Residues in contact with THR 99 (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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35B ILE* 4.8 3.8 - - + -
64B PHE* 3.7 22.5 - - + -
69B CYS 5.9 0.7 + - - -
72B GLU* 5.0 2.1 - - + +
73B ILE* 4.1 17.3 - - + +
76B LEU* 3.7 20.2 - - + -
95B LYS* 2.8 22.4 + - - +
96B THR 3.5 4.5 - - - -
98B ASP* 1.3 75.9 - - - +
100B ALA* 1.4 55.8 + - - +
102B ALA* 3.2 5.8 + - - +
103B ILE* 2.7 54.5 + - + +
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Residues in contact with ALA 100 (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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35B ILE* 4.1 8.7 - - + +
88B VAL* 3.8 21.1 - - + +
90B GLY* 3.6 34.8 - - - +
96B THR 2.8 13.0 + - - +
97B LEU 3.2 5.1 + - - +
99B THR* 1.4 75.9 - - - +
101B LYS* 1.3 55.2 + - - +
103B ILE 3.4 0.3 + - - -
104B ALA* 3.0 30.5 + - - +
111B VAL* 4.1 3.4 - - + -
113B LEU* 3.9 8.5 - - + -
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Residues in contact with LYS 101 (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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97B LEU* 3.0 20.6 + - - +
98B ASP* 3.7 13.1 + - - +
100B ALA* 1.3 73.2 - - - +
102B ALA* 1.3 67.7 + - - +
104B ALA* 3.9 5.0 - - - +
105B HIS* 3.0 25.6 + - - +
111B VAL* 4.6 7.9 - - + -
113B LEU* 3.6 31.0 - - + -
122B ALA* 2.9 25.9 + - - +
123B PRO* 3.7 4.0 - - - +
125B SER 2.8 27.7 + - - +
126B ALA* 5.7 0.2 - - - -
127B LEU 3.3 15.0 + - - +
128B SER* 4.1 13.5 - - - +
143B TYR* 4.3 19.0 - - + -
147B PRO* 4.1 6.5 - - + -
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Residues in contact with ALA 102 (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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73B ILE* 3.5 35.9 - - + -
98B ASP 3.1 11.7 + - - +
99B THR 3.2 2.4 + - - +
101B LYS* 1.3 80.1 - - - +
103B ILE* 1.3 63.4 + - - +
105B HIS* 3.2 1.9 + - - +
106B TYR* 2.9 35.4 + - + -
143B TYR* 3.3 25.9 + - - +
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Residues in contact with ILE 103 (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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33B LEU* 4.7 4.9 - - + -
35B ILE* 4.3 5.8 - - + -
73B ILE* 3.8 35.9 - - + +
76B LEU* 3.9 16.2 - - + -
77B GLY* 4.3 6.5 - - - +
80B LEU* 3.6 30.1 - - + -
88B VAL* 3.8 9.0 - - + -
99B THR* 2.7 55.3 + - + +
100B ALA 3.9 4.5 - - - +
101B LYS 3.3 0.2 - - - -
102B ALA* 1.3 76.8 - - - +
104B ALA* 1.3 64.2 + - - +
106B TYR* 3.3 2.3 + - - -
107B GLN* 3.0 30.1 + - + +
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Residues in contact with ALA 104 (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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88B VAL* 4.0 15.0 - - + -
100B ALA 3.0 18.0 + - - +
101B LYS 3.9 3.8 - - - +
103B ILE* 1.3 78.0 - - - +
105B HIS* 1.3 56.9 + - - +
107B GLN* 4.9 1.6 - - - -
108B GLN* 2.8 25.5 + - - -
109B LEU* 3.0 26.3 + - - +
111B VAL* 3.5 30.1 - - + -
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Residues in contact with HIS 105 (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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101B LYS 3.0 19.8 + - - +
102B ALA 3.5 2.0 - - - +
104B ALA* 1.3 76.1 - - - +
106B TYR* 1.3 96.7 + + - +
108B GLN* 2.8 38.6 + - - +
143B TYR* 3.6 26.2 - + + +
144B PRO* 3.7 36.8 - - + +
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Residues in contact with TYR 106 (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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70B HIS* 3.4 38.4 + + - -
73B ILE* 4.1 11.9 - - + -
102B ALA* 2.9 44.9 + - + +
103B ILE* 4.2 3.6 - - - +
105B HIS* 1.3 97.7 - + - +
107B GLN* 1.3 70.4 + - - +
108B GLN* 3.7 5.4 + - - +
141B LEU* 5.5 9.5 - - + +
143B TYR* 5.0 5.1 - + - -
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Residues in contact with GLN 107 (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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77B GLY* 3.8 28.1 + - - -
80B LEU* 4.1 16.8 - - + -
81B LYS* 2.9 44.0 + - - +
103B ILE* 3.0 23.0 + - + +
104B ALA 4.2 0.9 - - - +
106B TYR* 1.3 85.9 + - - +
108B GLN* 1.3 72.3 + - - +
109B LEU* 3.5 27.5 + - + +
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Residues in contact with GLN 108 (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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104B ALA 2.8 13.3 + - - -
105B HIS* 2.8 33.3 + - - +
106B TYR 4.4 5.7 - - - +
107B GLN* 1.3 78.1 - - - +
109B LEU* 1.3 63.7 + - - +
110B PRO* 4.8 0.5 - - - +
144B PRO* 6.1 0.3 - - - +
145B ARG* 6.3 0.6 - - - +
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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