Contacts of the helix formed by residues 105 - 122 (chain A) in PDB entry 6V65
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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88A THR* 3.4 8.0 - - - +
103A PHE* 3.3 3.2 - - - +
104A GLN* 1.3 82.2 - - - +
106A PRO* 1.3 77.3 - - - +
107A ALA* 3.2 18.9 + - - +
108A ASP* 3.0 25.4 + - - +
109A ALA 3.1 9.2 + - - -
1254B TYR* 5.1 2.0 - - - -
1464B ASP* 4.7 8.8 + - - +
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Residues in contact with PRO 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 4.5 13.9 - - + -
88A THR* 3.3 17.9 - - + +
105A SER* 1.3 87.1 - - - +
107A ALA* 1.3 52.4 + - - +
109A ALA* 3.0 5.0 + - + +
110A ARG* 2.7 63.2 + - + +
1254B TYR* 3.4 36.1 - - + +
1366B HIS* 4.2 16.8 - - + +
1370B GLN* 6.0 1.3 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A SER* 3.1 9.1 + - - +
106A PRO* 1.3 78.1 - - - +
108A ASP* 1.3 66.6 + - - +
110A ARG* 3.5 19.1 - - - +
111A ALA* 3.2 24.4 + - - +
202A FMT 4.7 9.2 - - - +
1366B HIS* 6.1 0.2 - - - -
1464B ASP* 3.3 25.3 + - - +
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Residues in contact with ASP 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A VAL* 3.5 28.6 - - + +
18A ARG* 4.7 11.3 + - - +
103A PHE* 3.9 9.0 - - + -
104A GLN* 4.8 11.6 - - - +
105A SER* 3.0 20.4 + - - +
107A ALA* 1.3 80.8 - - - +
109A ALA* 1.3 64.5 + - - +
111A ALA* 4.0 2.0 - - - -
112A PHE* 3.1 25.1 + - - +
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Residues in contact with ALA 109 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A PRO* 5.3 1.1 - - + -
88A THR* 3.7 22.2 - - - +
90A HIS* 3.5 21.9 - - + +
103A PHE* 3.5 35.1 - - + -
105A SER 3.1 5.7 + - - +
106A PRO* 3.0 9.7 + - + +
108A ASP* 1.3 75.0 - - - +
110A ARG* 1.3 65.3 + - + +
112A PHE* 3.5 1.7 + - - +
113A ASP* 3.1 17.2 + - - +
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Residues in contact with ARG 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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90A HIS* 5.5 0.2 - - - -
106A PRO* 2.7 46.5 + - + +
107A ALA* 3.5 28.3 - - - +
109A ALA* 1.3 74.4 - - + +
111A ALA* 1.3 57.6 + - - +
113A ASP* 3.2 7.8 + - - +
114A ARG* 3.0 36.8 + - + +
202A FMT 3.8 32.8 - - - +
1366B HIS* 4.7 13.7 + - - -
1370B GLN* 5.6 5.5 - - - +
1464B ASP* 4.9 5.7 + - - -
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Residues in contact with ALA 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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15A ALA* 3.9 8.0 - - - +
17A VAL* 5.2 4.9 - - + -
107A ALA 3.2 16.7 + - - +
108A ASP* 4.1 5.2 - - - +
110A ARG* 1.3 79.0 - - - +
112A PHE* 1.3 62.4 + - - +
114A ARG* 3.3 31.6 + - - +
115A GLY* 3.1 17.7 + - - -
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Residues in contact with PHE 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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15A ALA* 4.1 15.4 - - + +
17A VAL* 3.7 21.6 - - + +
42A VAL* 3.6 42.8 - - + -
44A VAL* 3.6 25.8 - - + -
60A ILE* 4.2 12.1 - - + -
82A TYR* 3.7 20.2 - + - -
92A TRP* 5.0 0.9 - + - -
101A LEU* 3.6 15.5 - - + -
103A PHE* 3.7 18.6 - + + -
108A ASP 3.1 18.8 + - - +
109A ALA 3.9 1.6 - - - +
110A ARG 3.3 0.2 - - - -
111A ALA* 1.3 76.7 - - - +
113A ASP* 1.3 62.3 + - - +
115A GLY* 3.4 1.4 + - - -
116A ILE* 3.4 33.0 + - + +
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Residues in contact with ASP 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A TYR* 3.5 22.7 + - + -
84A LYS* 2.7 43.6 + - + +
90A HIS* 4.3 5.2 - - + -
109A ALA 3.1 15.1 + - - +
110A ARG* 3.2 10.5 + - - +
112A PHE* 1.3 75.8 - - - +
114A ARG* 1.3 66.0 + - - +
116A ILE* 3.5 7.2 + - - +
117A ARG* 3.0 26.5 + - - +
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ARG* 3.0 20.2 + - + +
111A ALA* 3.3 32.6 + - - +
113A ASP* 1.3 76.9 - - + +
115A GLY* 1.3 62.0 + - - +
117A ARG* 3.8 5.8 - - - +
118A ARG* 3.3 28.2 + - + +
202A FMT 5.1 7.5 + - - -
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Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.6 37.3 - - - -
15A ALA* 4.0 4.9 - - - -
44A VAL* 4.7 1.1 - - - -
111A ALA 3.1 13.0 + - - -
112A PHE 3.4 3.5 + - - -
113A ASP 3.2 0.6 - - - -
114A ARG* 1.3 79.4 - - - +
116A ILE* 1.3 57.4 + - - +
118A ARG* 3.4 1.8 + - - +
119A ALA* 3.0 25.3 + - - +
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Residues in contact with ILE 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 3.5 29.2 - - + -
60A ILE* 4.7 12.6 - - + -
76A LEU* 4.5 11.9 - - + -
80A LEU* 6.1 2.5 - - + -
82A TYR* 3.5 55.4 - - + +
112A PHE* 3.4 22.4 + - + +
113A ASP* 3.5 11.7 - - - +
115A GLY* 1.3 73.1 - - - +
117A ARG* 1.3 67.1 + - - +
119A ALA* 3.6 8.4 - - - +
120A ILE* 3.1 35.9 + - + +
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Residues in contact with ARG 117 (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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113A ASP* 3.0 24.6 + - - +
114A ARG* 3.8 8.1 - - - +
115A GLY 3.2 0.2 - - - -
116A ILE* 1.3 78.9 - - - +
118A ARG* 1.3 65.9 + - - +
120A ILE* 3.6 6.0 + - - +
121A GLU* 3.3 19.2 + - - +
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Residues in contact with ARG 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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14A TYR* 4.3 10.3 - - + -
114A ARG* 3.3 17.8 + - + +
115A GLY* 4.0 4.0 - - - +
117A ARG* 1.3 79.5 - - - +
119A ALA* 1.3 66.3 + - - +
121A GLU* 3.1 35.6 + - - +
122A ASP* 3.1 27.8 + - - +
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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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14A TYR* 3.9 19.7 - - + -
44A VAL* 4.1 8.3 - - + -
58A PHE* 3.8 16.7 - - + -
76A LEU* 3.8 22.4 - - + -
115A GLY 3.0 17.9 + - - +
116A ILE* 3.6 7.9 - - - +
117A ARG 3.3 0.2 - - - -
118A ARG* 1.3 77.2 - - - +
120A ILE* 1.3 61.5 + - - +
122A ASP* 3.1 12.6 + - - +
123A ILE* 3.5 13.1 + - - +
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Residues in contact with ILE 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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76A LEU* 4.7 12.8 - - + -
77A LYS 3.7 18.2 - - - +
78A LYS* 3.9 35.7 - - + +
80A LEU* 4.6 23.1 - - + +
82A TYR* 6.1 3.4 - - + -
116A ILE* 3.1 23.0 + - + +
117A ARG* 4.0 6.1 - - - +
119A ALA* 1.3 76.0 - - - +
121A GLU* 1.3 62.8 + - - +
123A ILE* 3.2 26.2 + - + +
124A SER 4.9 0.2 + - - -
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Residues in contact with GLU 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 ARG 3.3 14.0 + - - +
118A ARG* 3.1 47.6 + - - +
119A ALA 3.2 0.6 - - - -
120A ILE* 1.3 77.2 - - - +
122A ASP* 1.3 66.0 + - - +
123A ILE 3.4 1.5 + - - -
124A SER 4.8 2.8 + - - -
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Residues in contact with ASP 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A TYR* 3.2 25.2 + - - +
46A LYS* 5.7 0.2 + - - -
56A ALA 5.8 0.5 + - - -
58A PHE* 3.1 23.2 - - + -
118A ARG* 3.1 14.0 + - - +
119A ALA 3.1 5.9 + - - +
120A ILE 3.1 0.8 - - - -
121A GLU* 1.3 90.9 - - - +
123A ILE* 1.3 62.2 + - - +
124A SER 3.5 1.3 - - - -
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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