Contacts of the helix formed by residues 97 - 111 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A MET* 3.5 25.6 - - + -
90A VAL* 3.8 20.2 + - + -
92A PHE* 4.0 18.6 - + - -
96A THR* 1.3 83.3 + - - +
98A GLU* 1.3 65.7 + - - +
99A PRO* 3.3 9.4 - - + +
100A ALA* 3.2 39.9 + - + +
101A ALA* 3.2 21.1 + - - +
321A ALA 2.9 29.5 + - - -
323A PRO* 3.5 28.0 - - + +
326A CYS* 4.7 0.2 - - - -
13B ILE* 4.0 8.8 - - - +
37B VAL* 4.8 1.1 - - - -
38B ALA* 3.7 7.9 - - + +
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Residues in contact with GLU 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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97A HIS* 1.3 67.9 - - - +
99A PRO* 1.4 69.9 - - + +
101A ALA* 3.2 1.0 + - - +
102A ARG* 2.8 60.1 + - + +
8B LEU* 2.9 46.0 + - + +
13B ILE* 3.8 19.8 - - + +
38B ALA 4.7 2.6 + - - -
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Residues in contact with PRO 99 (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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83A GLN* 3.5 37.9 - - - +
87A MET* 4.9 1.8 - - + -
97A HIS* 3.3 19.3 - - + +
98A GLU* 1.4 94.5 - - + +
100A ALA* 1.3 61.0 + - - +
102A ARG* 3.4 6.4 + - + +
103A LEU* 2.9 27.2 + - - +
323A PRO* 3.7 11.9 - - + +
326A CYS* 3.6 21.8 - - + +
327A ALA* 4.0 8.7 - - + +
330A VAL* 4.0 4.5 - - + +
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Residues in contact with ALA 100 (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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92A PHE* 3.8 27.6 - - + -
97A HIS* 3.2 30.9 + - + +
98A GLU 3.3 0.2 - - - -
99A PRO* 1.3 78.5 - - - +
101A ALA* 1.3 58.4 + - - +
103A LEU* 3.9 0.3 - - - -
104A ALA* 2.9 31.4 + - - +
120A PHE* 4.0 7.3 - - + -
321A ALA* 4.1 8.5 - - + +
326A CYS* 4.1 9.4 - - - -
21B LEU* 3.9 6.3 - - + +
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Residues in contact with ALA 101 (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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97A HIS 3.2 14.7 + - - +
98A GLU 3.2 4.9 + - - +
100A ALA* 1.3 74.4 - - - +
102A ARG* 1.3 67.3 + - - +
104A ALA* 3.3 0.9 + - - +
105A LYS* 3.0 20.8 + - - +
8B LEU* 3.9 15.3 - - + -
13B ILE* 4.1 18.4 - - + +
16B VAL* 3.3 32.1 - - + +
21B LEU* 4.0 10.5 - - + +
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Residues in contact with ARG 102 (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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98A GLU* 2.8 48.3 + - + +
99A PRO* 3.9 4.5 - - + +
101A ALA* 1.3 72.8 - - - +
103A LEU* 1.3 63.7 + - - +
105A LYS* 3.5 5.0 + - - +
106A LEU* 3.1 27.2 + - + +
330A VAL* 3.7 23.3 - - + +
334A GLU* 3.0 36.8 + - - -
8B LEU* 3.8 24.2 - - + +
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Residues in contact with LEU 103 (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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99A PRO 2.9 17.9 + - - +
100A ALA 4.0 2.2 - - - +
102A ARG* 1.3 76.0 - - - +
104A ALA* 1.3 64.3 + - - +
106A LEU* 3.2 8.3 + - + +
107A LEU* 3.0 40.6 + - + +
120A PHE* 3.5 28.9 - - + -
285A LEU* 4.2 9.0 - - + -
292A LEU* 3.7 14.4 - - + -
326A CYS* 3.9 10.3 - - - +
329A SER* 3.6 37.0 - - - +
330A VAL* 3.7 20.1 - - + +
333A VAL* 4.6 6.5 - - + -
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Residues in contact with ALA 104 (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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100A ALA 2.9 18.8 + - - +
101A ALA* 3.7 3.8 - - - +
103A LEU* 1.3 76.0 - - - +
105A LYS* 1.3 58.1 + - - +
107A LEU* 3.4 2.1 + - - +
108A VAL* 2.9 34.9 + - - +
118A VAL* 4.0 13.6 - - + +
120A PHE* 4.2 4.4 - - + -
16B VAL* 4.7 1.3 - - + -
20B HIS* 4.3 14.1 - - + -
21B LEU* 3.5 30.1 - - + -
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Residues in contact with LYS 105 (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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101A ALA 3.0 16.9 + - - +
102A ARG* 3.8 5.4 - - - +
104A ALA* 1.3 76.5 - - - +
106A LEU* 1.3 61.9 + - + +
108A VAL* 3.6 1.4 + - - +
109A ASP* 2.9 57.7 + - - +
8B LEU* 6.1 5.6 - - + -
16B VAL* 4.1 26.1 - - + +
20B HIS* 4.7 16.5 + - + +
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Residues in contact with LEU 106 (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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102A ARG* 3.1 18.4 + - + +
103A LEU* 3.2 10.3 + - + +
105A LYS* 1.3 74.7 - - - +
107A LEU* 1.3 58.8 + - + +
109A ASP* 3.2 8.7 + - + +
110A ILE* 3.0 35.5 + - + +
330A VAL* 4.0 30.5 - - + +
333A VAL* 4.2 14.1 - - + -
334A GLU* 4.0 30.7 - - + +
337A LEU* 4.1 26.5 - - + -
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Residues in contact with LEU 107 (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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103A LEU* 3.0 38.8 + - + +
104A ALA 3.9 3.1 - - - +
106A LEU* 1.3 74.3 - - - +
108A VAL* 1.3 59.1 + - - +
110A ILE* 4.0 9.6 - - + -
111A THR* 2.6 44.6 + - + +
118A VAL* 4.4 6.1 - - + -
120A PHE* 4.0 18.6 - - + -
260A PHE* 3.8 33.7 - - + -
267A PHE* 5.2 0.2 - - + -
281A VAL* 4.7 7.2 - - + -
285A LEU* 3.9 13.7 - - + -
294A ALA* 4.2 14.8 - - + -
296A LEU* 4.2 14.1 - - + -
333A VAL* 4.9 2.0 - - + -
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Residues in contact with VAL 108 (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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104A ALA 2.9 19.7 + - - +
105A LYS* 4.1 2.9 - - - +
107A LEU* 1.3 77.8 - - - +
109A ASP* 1.3 68.4 + - - +
111A THR* 3.6 11.3 + - - +
112A PRO 5.2 0.7 - - - +
115A LEU 3.6 25.6 - - - +
116A ASP* 3.7 26.0 - - - +
118A VAL* 3.7 20.4 - - + -
296A LEU* 4.4 0.9 - - + -
20B HIS* 3.7 32.3 - - + +
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Residues in contact with ASP 109 (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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105A LYS* 2.9 52.3 + - - +
106A LEU* 3.2 7.0 + - + +
108A VAL* 1.3 84.7 - - - +
110A ILE* 1.3 63.7 + - + +
111A THR 3.9 3.9 + - - +
20B HIS* 5.9 0.3 + - - -
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Residues in contact with ILE 110 (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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106A LEU* 3.0 24.0 + - + +
107A LEU* 4.0 11.0 - - + +
109A ASP* 1.3 79.6 - - + +
111A THR* 1.3 65.1 + - - +
112A PRO* 4.6 0.2 - - - +
260A PHE* 4.0 13.5 - - + -
266A LEU* 3.7 24.3 - - + +
267A PHE* 3.3 37.3 - - + -
270A ASP* 4.9 2.9 - - - +
333A VAL* 3.9 24.2 - - + -
336A LEU* 6.4 0.4 - - + -
337A LEU* 3.7 32.5 - - + -
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Residues in contact with THR 111 (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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107A LEU* 2.6 31.7 + - + +
108A VAL* 3.6 12.6 + - - +
109A ASP 3.6 3.8 - - - +
110A ILE* 1.3 81.4 - - - +
112A PRO* 1.3 76.3 + - - +
113A ALA* 3.5 2.1 + - - -
115A LEU* 3.9 11.5 + - - +
267A PHE* 3.7 25.1 - - + -
270A ASP* 5.3 0.2 - - - -
279A MET* 4.0 18.8 - - + -
281A VAL* 5.1 1.6 - - + -
296A LEU* 3.7 20.8 - - + +
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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