Contacts of the helix formed by residues 97 - 111 (chain B) in PDB entry 4MQP
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 HIS 97 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 4.1 8.5 - - - -
37A VAL* 4.9 0.9 - - - -
38A ALA* 3.6 7.0 - - + +
87B MET* 3.6 25.6 - - + -
90B VAL* 3.8 26.2 + - + -
91B MET 5.5 0.2 - - - -
92B PHE* 3.9 19.1 - + - -
95B LEU 5.4 0.2 - - - -
96B THR* 1.3 84.3 + - - +
98B GLU* 1.3 66.3 + - - +
99B PRO* 3.4 9.0 - - + +
100B ALA* 3.2 40.7 + - + +
101B ALA* 3.1 22.2 + - - +
321B ALA 2.9 29.5 + - - -
323B PRO* 3.7 19.1 - - + +
326B CYS* 4.8 0.4 - - - -
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Residues in contact with GLU 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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8A LEU* 2.9 42.3 + - + +
13A ILE* 3.8 24.0 - - + +
38A ALA 4.7 2.2 + - - -
97B HIS* 1.3 71.6 - - - +
99B PRO* 1.4 67.2 - - + +
101B ALA* 3.2 0.9 + - - -
102B ARG* 2.8 58.4 + - + +
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Residues in contact with PRO 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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83B GLN* 3.4 37.5 - - - +
87B MET* 5.1 2.0 - - + -
97B HIS* 3.4 17.3 - - + +
98B GLU* 1.4 92.1 - - + +
100B ALA* 1.3 61.3 + - - +
102B ARG* 4.7 5.6 - - + -
103B LEU* 3.0 26.9 + - - +
323B PRO* 3.7 12.6 - - + +
326B CYS* 3.6 22.2 - - + +
327B ALA* 3.9 9.6 - - + +
330B VAL* 3.9 5.8 - - + +
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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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21A LEU* 3.9 8.4 - - + +
92B PHE* 3.8 27.4 - - + -
97B HIS* 3.2 32.1 + - + +
98B GLU 3.3 0.2 - - - -
99B PRO* 1.3 78.6 - - - +
101B ALA* 1.3 58.7 + - - +
103B LEU* 3.4 0.5 + - - -
104B ALA* 2.9 31.7 + - - +
120B PHE* 3.9 5.1 - - + -
321B ALA* 4.1 7.6 - - + -
326B CYS* 4.1 9.2 - - - +
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Residues in contact with ALA 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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8A LEU* 4.1 13.7 - - + -
13A ILE* 4.0 21.8 - - + +
16A VAL* 3.4 27.1 - - + +
21A LEU* 3.9 13.0 - - + +
97B HIS 3.1 16.8 + - - +
98B GLU 3.2 3.6 + - - +
100B ALA* 1.3 73.6 - - - +
102B ARG* 1.3 66.4 + - - +
104B ALA 3.3 0.7 + - - -
105B LYS* 3.0 21.0 + - - +
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Residues in contact with ARG 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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8A LEU* 3.9 24.9 - - + +
98B GLU* 2.8 48.8 + - + +
99B PRO* 4.0 2.0 - - + +
101B ALA* 1.3 71.7 - - - +
103B LEU* 1.3 57.4 + - - +
105B LYS* 3.6 5.2 + - - +
106B LEU* 3.1 31.8 + - + +
330B VAL* 3.5 29.2 - - + +
334B GLU* 3.3 34.2 + - - -
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Residues in contact with LEU 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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99B PRO 3.0 18.6 + - - +
100B ALA 3.9 0.2 - - - +
102B ARG* 1.3 75.8 - - - +
104B ALA* 1.3 60.2 + - - +
106B LEU* 3.3 6.0 + - + +
107B LEU* 2.9 50.3 + - + +
120B PHE* 3.6 32.8 - - + -
285B LEU* 4.5 6.1 - - + -
292B LEU* 3.7 12.8 - - + -
326B CYS* 3.9 9.9 - - + -
329B SER* 3.6 37.2 - - - +
330B VAL* 3.6 19.5 - - + +
333B VAL* 4.5 6.3 - - + -
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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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16A VAL* 4.8 1.1 - - + -
20A HIS* 4.3 10.3 - - + -
21A LEU* 3.7 29.6 - - + -
100B ALA 2.9 18.9 + - - +
101B ALA* 3.8 3.4 - - - +
103B LEU* 1.3 76.4 - - - +
105B LYS* 1.3 58.2 + - - +
107B LEU* 3.3 1.5 + - - +
108B VAL* 2.9 36.9 + - - +
118B VAL* 4.0 18.6 - - + +
120B PHE* 4.1 4.9 - - + -
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Residues in contact with LYS 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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8A LEU* 6.0 7.2 - - + -
16A VAL* 4.1 27.2 - - + +
20A HIS* 5.0 11.1 + - + +
101B ALA 3.0 16.6 + - - +
102B ARG* 3.8 5.8 - - - +
104B ALA* 1.3 77.7 - - - +
106B LEU* 1.3 61.9 + - - +
108B VAL* 3.6 4.8 + - - +
109B ASP* 2.9 58.5 + - - +
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Residues in contact with LEU 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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102B ARG* 3.1 22.1 + - + +
103B LEU* 3.6 8.5 - - + +
105B LYS* 1.3 76.2 - - + +
107B LEU* 1.3 62.0 + - - +
109B ASP* 3.1 6.0 + - + +
110B ILE* 3.1 31.1 + - + +
330B VAL* 4.0 38.6 - - + +
333B VAL* 4.1 16.4 - - + -
334B GLU* 4.0 22.4 - - + +
337B LEU* 4.1 25.6 - - + -
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Residues in contact with LEU 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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103B LEU* 2.9 33.4 + - + +
104B ALA 3.9 3.6 - - - +
106B LEU* 1.3 74.2 - - + +
108B VAL* 1.3 56.6 + - - +
110B ILE* 4.1 8.7 - - + -
111B THR* 2.6 45.2 + - + +
118B VAL* 4.3 7.2 - - + -
120B PHE* 4.0 26.5 - - + -
260B PHE* 4.0 32.1 - - + -
281B VAL* 4.7 6.1 - - + -
285B LEU* 4.0 12.3 - - + -
294B ALA* 4.1 17.0 - - + -
296B LEU* 4.0 14.1 - - + -
333B VAL* 4.9 2.7 - - + -
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Residues in contact with VAL 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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20A HIS* 3.8 30.3 - - + +
104B ALA 2.9 20.9 + - - +
105B LYS* 4.1 4.0 - - - +
107B LEU* 1.3 77.7 - - - +
109B ASP* 1.3 67.7 + - - +
110B ILE 3.4 0.5 + - - -
111B THR* 3.4 12.2 + - - +
112B PRO 5.2 0.9 - - - +
115B LEU 3.4 25.5 - - - +
116B ASP* 3.7 26.0 - - - +
117B THR 4.3 0.2 - - - +
118B VAL* 3.7 20.0 - - + -
296B LEU* 4.4 1.3 - - + -
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Residues in contact with ASP 109 (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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105B LYS* 2.9 52.0 + - - +
106B LEU* 3.1 7.9 + - + +
108B VAL* 1.3 82.2 - - - +
110B ILE* 1.3 64.5 + - + +
111B THR 4.4 2.1 - - - +
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Residues in contact with ILE 110 (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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106B LEU* 3.1 17.9 + - + +
107B LEU* 3.9 11.2 - - + +
109B ASP* 1.3 82.3 - - + +
111B THR* 1.3 68.2 + - - +
112B PRO* 4.6 0.2 - - - +
260B PHE* 4.2 11.2 - - + -
266B LEU* 3.7 22.4 - - + +
267B PHE* 3.5 36.6 - - + -
270B ASP* 4.8 3.8 - - - +
333B VAL* 3.9 25.6 - - + -
336B LEU* 6.3 0.2 - - + -
337B LEU* 3.7 32.1 - - + -
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Residues in contact with THR 111 (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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107B LEU* 2.6 27.8 + - + +
108B VAL 3.4 12.8 + - - +
109B ASP 4.4 2.6 - - - +
110B ILE* 1.3 82.4 + - + +
112B PRO* 1.4 76.0 + - - +
113B ALA* 3.5 2.3 + - - -
115B LEU* 3.8 16.0 - - - +
267B PHE* 4.0 22.7 - - + -
270B ASP* 5.4 0.4 - - - -
279B MET* 4.0 15.7 - - + -
281B VAL* 5.1 1.6 - - + -
296B LEU* 3.6 26.2 - - + +
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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