Contacts of the helix formed by residues 105 - 124 (chain A) in PDB entry 5MQI
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 SER 105 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103A GLU* 3.0 29.5 + - - +
104A PRO* 1.3 77.2 - - - +
106A PHE* 1.3 78.8 + - - -
107A ARG 3.0 0.7 - - - -
108A HIS* 2.8 18.8 + - - +
109A HIS* 3.3 21.6 + - - -
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Residues in contact with PHE 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A GLU* 3.5 43.1 - - + -
48A THR* 4.2 7.9 - - - -
97A PHE* 4.5 10.2 - + - -
101A PRO* 3.4 26.2 - - + +
103A GLU* 3.4 31.8 + - - +
105A SER* 1.3 86.7 + - - +
107A ARG* 1.3 57.2 + - - +
109A HIS* 3.0 18.3 + + - +
110A PHE 2.8 26.9 + - - -
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Residues in contact with ARG 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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101A PRO* 3.2 29.9 - - + +
102A LYS 5.3 3.8 + - - -
103A GLU 3.0 20.7 + - - +
104A PRO* 4.3 7.2 - - + +
105A SER 3.0 1.0 - - - -
106A PHE* 1.3 76.8 - - - +
108A HIS* 1.3 62.2 + - - +
110A PHE* 3.8 2.7 - - + +
111A LEU* 3.1 49.4 + - + +
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Residues in contact with HIS 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A GLN* 4.6 7.6 + - - -
104A PRO 3.7 12.0 + - - +
105A SER* 2.8 11.3 + - - +
107A ARG* 1.3 77.8 - - - +
109A HIS* 1.3 69.4 + + - +
111A LEU* 3.9 7.5 - - - +
112A GLN* 3.0 50.4 + - - +
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Residues in contact with HIS 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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48A THR* 3.1 38.6 + - + +
53A GLN* 3.8 27.4 - - - +
97A PHE* 3.7 20.2 - - + -
105A SER* 3.9 18.1 + - - -
106A PHE* 3.0 28.5 + + - +
108A HIS* 1.3 81.2 - + - +
110A PHE* 1.3 58.8 + - - +
112A GLN* 2.6 25.8 + - - +
113A VAL* 2.8 13.4 + - - +
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Residues in contact with PHE 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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93A ALA* 3.6 34.4 - - + +
94A LEU* 3.9 17.7 - - + -
97A PHE* 3.5 30.3 - + + -
99A ASN 4.3 6.5 - - - -
100A LEU* 3.5 30.5 - - + -
101A PRO* 3.5 26.0 - - + -
106A PHE 2.8 19.1 + - - +
107A ARG* 3.8 4.9 - - - +
109A HIS* 1.3 72.0 - - - +
111A LEU* 1.3 71.7 + - + +
113A VAL* 3.3 4.0 + - - +
114A LEU* 2.9 38.2 + - + +
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Residues in contact with LEU 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 ARG* 3.1 47.1 + - + +
108A HIS* 4.0 6.5 - - - +
110A PHE* 1.3 96.6 - - + +
112A GLN* 1.3 60.4 + - - +
114A LEU* 3.8 15.3 - - + +
115A THR* 2.8 31.4 + - - -
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Residues in contact with GLN 112 (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 GLN* 3.4 28.5 - - - +
108A HIS* 3.0 34.6 + - - +
109A HIS 2.6 14.6 + - - +
111A LEU* 1.3 70.7 - - - +
113A VAL* 1.3 64.7 + - - +
115A THR* 3.2 15.6 + - - +
116A TYR* 2.8 63.9 + - + +
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Residues in contact with VAL 113 (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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49A ARG* 4.5 3.1 - - + +
52A ARG* 4.1 35.2 - - + -
53A GLN* 4.7 11.0 - - + +
91A GLN 5.2 0.4 - - - +
93A ALA* 3.7 26.2 - - + -
96A CYS* 4.6 4.5 - - - -
97A PHE* 3.4 31.9 - - + -
109A HIS 2.8 11.6 + - - +
110A PHE 3.5 6.7 - - - +
112A GLN* 1.3 71.2 - - - +
114A LEU* 1.3 59.1 + - - +
116A TYR* 3.2 10.5 + - - +
117A LEU* 3.0 34.1 + - + +
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Residues in contact with LEU 114 (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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93A ALA* 4.6 8.7 - - + -
110A PHE* 2.9 30.2 + - + +
111A LEU* 3.8 17.3 - - + +
113A VAL* 1.3 77.2 - - - +
115A THR* 1.3 55.9 + - - +
117A LEU* 3.2 19.0 + - + -
118A GLN* 2.9 43.8 + - + +
170A PRO* 3.6 41.1 - - + +
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Residues in contact with THR 115 (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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111A LEU 2.8 22.9 + - - -
112A GLN* 3.2 22.7 + - - +
114A LEU* 1.3 75.7 - - - +
116A TYR* 1.3 69.5 + - + +
118A GLN* 3.5 13.5 + - - +
119A ALA* 3.2 21.5 + - + +
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Residues in contact with TYR 116 (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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52A ARG 4.4 2.5 - - - +
53A GLN* 3.6 26.9 + - + +
56A GLY* 3.4 20.9 - - - -
57A ALA* 3.4 34.2 - - - +
112A GLN* 2.8 58.6 + - + +
113A VAL* 3.6 9.6 - - - +
115A THR* 1.3 82.4 - - + +
117A LEU* 1.3 59.2 + - - +
119A ALA* 3.1 8.5 + - + +
120A TYR* 2.9 53.7 + + + +
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Residues in contact with LEU 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU 3.5 23.1 - - - +
90A THR* 3.7 15.3 - - + +
91A GLN 3.4 28.0 - - - +
92A PRO* 4.0 4.9 - - + -
93A ALA* 3.6 27.6 - - + +
113A VAL* 3.0 20.1 + - + +
114A LEU* 3.2 16.8 + - + +
116A TYR* 1.3 75.6 - - - +
118A GLN* 1.3 62.0 + - - +
120A TYR* 3.1 10.5 + - + +
121A LYS* 2.9 23.0 + - - +
169A VAL* 3.9 27.0 - - + +
170A PRO* 5.8 1.8 - - + +
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Residues in contact with GLN 118 (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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114A LEU* 2.9 35.1 + - - +
115A THR* 3.8 13.4 + - - +
116A TYR 3.3 0.2 - - - -
117A LEU* 1.3 71.6 - - - +
119A ALA* 1.3 63.8 + - - +
121A LYS* 3.3 6.6 + - + +
122A GLU* 3.2 26.7 + - - +
169A VAL* 3.9 17.5 - - + +
170A PRO* 3.7 28.4 - - + +
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Residues in contact with ALA 119 (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 GLN* 6.2 0.7 - - - +
62A GLN* 3.9 19.6 + - - +
115A THR* 3.2 13.3 + - + +
116A TYR* 3.1 14.1 + - + +
118A GLN* 1.3 75.0 - - - +
120A TYR* 1.3 66.4 + - + +
122A GLU* 3.2 7.7 + - - +
123A ALA* 3.0 22.0 + - - +
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Residues in contact with TYR 120 (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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52A ARG 4.5 2.8 + - - -
55A LEU 4.2 3.1 + - - -
56A GLY* 3.3 30.4 + - - -
61A LEU* 3.6 48.7 + - + +
62A GLN* 3.6 21.1 - - - -
89A LEU* 3.5 42.1 - - + +
90A THR* 4.3 4.7 - - + -
116A TYR* 2.9 34.1 + + + +
117A LEU* 3.1 13.7 + - + +
119A ALA* 1.3 75.3 - - - +
121A LYS* 1.3 62.2 + - - +
123A ALA* 3.2 6.8 + - - +
124A PHE* 3.0 31.4 + - - -
166A ILE* 4.5 12.3 - - + -
169A VAL* 6.2 0.2 - - + -
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Residues in contact with LYS 121 (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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117A LEU 2.9 12.9 + - - +
118A GLN* 3.5 12.1 - - + +
119A ALA 3.2 0.2 - - - -
120A TYR* 1.3 76.3 - - - +
122A GLU* 1.3 61.3 + - + +
124A PHE* 3.4 8.1 + - - +
125A ALA* 3.5 8.5 + - - +
166A ILE* 3.0 38.8 + - - +
167A LEU* 3.1 5.3 + - - +
169A VAL* 2.7 42.6 + - + +
170A PRO* 5.3 1.8 - - + -
185A ALA* 4.1 14.2 - - + +
186A HIS* 3.0 52.3 + - - +
189A LEU* 3.7 18.6 - - + +
227A ARG* 4.8 0.7 - - - +
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Residues in contact with GLU 122 (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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118A GLN 3.2 13.3 + - - +
119A ALA* 3.2 10.1 + - - +
121A LYS* 1.3 75.5 - - - +
123A ALA* 1.3 65.2 + - - +
125A ALA* 3.1 24.2 + - - +
185A ALA* 4.1 24.4 - - + +
188A GLN* 6.1 3.8 - - - +
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Residues in contact with ALA 123 (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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61A LEU* 4.7 1.3 - - + -
62A GLN* 3.9 22.0 - - + -
66A LEU* 3.6 30.6 - - + +
119A ALA 3.0 13.7 + - - +
120A TYR* 3.2 9.8 + - - +
122A GLU* 1.3 76.2 - - - +
124A PHE* 1.3 60.3 + - - +
125A ALA 3.3 1.6 + - - +
126A SER* 4.0 13.9 + - - -
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Residues in contact with PHE 124 (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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61A LEU* 4.0 27.8 - - + -
66A LEU* 4.1 15.7 - - + -
69A LEU* 4.9 1.6 - - + -
86A MET* 3.9 25.4 - - + -
120A TYR* 3.0 26.0 + - + +
121A LYS 3.8 5.8 - - - +
122A GLU 3.2 0.6 - - - -
123A ALA* 1.3 74.5 - - - +
125A ALA* 1.3 50.6 + - - +
126A SER* 2.5 24.4 + - - +
129A ALA* 4.3 15.4 - - + +
130A PHE* 3.5 30.2 - + + -
133A LEU* 4.6 9.2 - - + -
162A LEU* 4.1 27.4 - - + -
166A ILE* 3.4 32.5 - - + -
189A LEU* 3.7 13.5 - - + -
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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
------------------------------------------------------------
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