Contacts of the helix formed by residues 110 - 126 (chain A) in PDB entry 4A12
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 ARG 110 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A SER 4.7 0.4 + - - -
100A ASP* 2.7 33.9 + - - +
101A SER* 3.0 13.0 + - - +
102A VAL 2.7 28.7 + - - -
103A PHE* 3.5 40.6 - - + +
109A ALA* 1.3 72.7 - - - +
111A GLY* 1.3 65.8 + - - +
112A HIS* 3.3 32.3 + - + -
113A VAL* 3.1 25.9 + - + +
114A LEU* 3.9 5.8 + - - +
77B GLU* 3.1 56.4 + - - +
119B ASN* 5.2 0.2 - - - +
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Residues in contact with GLY 111 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PHE* 4.9 3.8 - - - -
109A ALA 3.8 2.0 + - - -
110A ARG* 1.3 71.6 - - - +
112A HIS* 1.3 60.3 + - - +
113A VAL 3.3 1.2 + - - -
114A LEU 3.5 5.9 + - - -
115A PHE* 3.5 4.9 + - - +
140A PHE* 3.3 41.7 - - - -
115B PHE* 4.2 3.1 - - - -
119B ASN* 3.7 18.2 + - - -
133B THR* 4.5 8.5 + - - +
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Residues in contact with HIS 112 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ILE* 3.4 31.0 - - + +
103A PHE* 6.1 0.4 - + - -
110A ARG* 3.6 38.5 + - + +
111A GLY* 1.3 71.1 - - - +
113A VAL* 1.3 66.5 + - + +
114A LEU 3.5 0.2 - - - -
115A PHE* 3.9 1.5 - - - +
116A ALA* 2.9 31.5 + - - +
77B GLU 4.7 2.2 + - - -
79B ILE* 4.2 9.9 - - + +
112B HIS* 5.2 1.5 - - - +
115B PHE* 3.7 19.3 - - + -
116B ALA* 3.6 33.7 + - + -
119B ASN* 3.4 17.5 + - + +
120B SER* 3.9 19.2 + - - -
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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
----------------------------------------------------------
73A ILE* 4.4 16.2 - - + -
79A ILE* 4.2 1.2 - - - +
95A LEU* 3.9 21.8 - - + +
97A ILE* 4.3 8.1 - - + -
100A ASP 5.6 0.2 - - - +
101A SER* 3.5 47.6 - - - +
109A ALA* 4.9 3.4 - - + -
110A ARG* 3.1 25.7 + - + +
112A HIS* 1.3 85.2 - - + +
114A LEU* 1.3 60.4 + - - +
116A ALA* 3.4 7.9 + - - +
117A GLN* 3.3 20.8 + - - +
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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
----------------------------------------------------------
95A LEU* 5.3 1.3 - - + -
97A ILE* 5.3 1.6 - - + -
109A ALA* 4.2 17.7 - - + +
110A ARG 4.3 7.0 - - - +
111A GLY 3.5 6.0 + - - +
113A VAL* 1.3 75.7 - - + +
115A PHE* 1.3 63.6 + - - +
117A GLN* 3.5 11.1 + - - +
118A ALA* 3.2 21.7 + - - +
140A PHE* 4.2 15.3 - - + -
144A VAL* 3.8 35.7 - - + +
150A VAL* 3.7 34.3 - - + -
170A SER* 4.8 2.9 + - - -
177A VAL* 4.6 0.7 - - + +
178A PHE* 4.1 33.9 - - + -
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Residues in contact with PHE 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 GLY 3.5 5.0 + - - +
112A HIS 3.9 1.8 - - - +
113A VAL 3.4 0.4 - - - -
114A LEU* 1.3 75.0 - - - +
116A ALA* 1.3 57.6 + - - +
118A ALA* 3.2 4.5 + - - +
119A ASN* 2.8 45.9 + - + +
136A SER* 3.4 26.5 - - - -
138A ILE* 3.7 31.0 - - + -
178A PHE* 4.3 4.8 - - - -
182A PHE* 3.5 20.9 - + - -
111B GLY 4.3 1.6 - - - -
112B HIS* 3.9 21.5 - - + -
115B PHE* 3.6 50.5 - + + -
138B ILE* 3.5 21.3 - - + -
140B PHE* 4.7 3.6 - + - -
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Residues in contact with ALA 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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73A ILE* 3.7 26.2 - - + -
79A ILE* 3.7 16.7 - - + +
112A HIS 2.9 19.9 + - - +
113A VAL 3.4 6.7 - - - +
115A PHE* 1.3 75.8 - - - +
117A GLN* 1.4 55.0 + - - +
119A ASN* 4.0 0.9 - - - +
120A SER* 3.0 34.7 + - - -
112B HIS* 3.7 20.0 + - + -
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Residues in contact with GLN 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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79A ILE* 3.6 19.5 - - + +
80A GLY* 4.8 0.2 - - - -
93A SER* 3.2 33.8 + - - +
94A ILE 3.7 0.2 - - - -
95A LEU* 3.5 32.1 - - + +
113A VAL 3.3 9.3 + - - +
114A LEU* 3.8 11.6 - - - +
115A PHE 3.3 0.2 - - - -
116A ALA* 1.4 78.4 - - - +
118A ALA* 1.3 57.2 + - - +
120A SER* 3.7 2.3 - - - -
121A LEU* 3.1 29.5 + - - +
150A VAL* 3.1 47.3 + - - +
152A ALA* 3.5 13.9 - - + +
170A SER* 4.4 1.9 + - - -
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Residues in contact with ALA 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 3.2 11.7 + - - +
115A PHE 3.2 8.0 + - - +
117A GLN* 1.3 75.7 - - - +
119A ASN* 1.3 64.7 + - - +
121A LEU* 3.3 8.2 + - - +
122A CYS* 3.2 25.3 + - - -
152A ALA* 5.3 1.8 - - - +
168A VAL* 3.9 18.4 - - + +
170A SER* 5.3 1.5 + - - +
178A PHE* 3.7 25.6 - - + -
182A PHE* 3.7 16.2 - - + -
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Residues in contact with ASN 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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115A PHE* 2.8 33.9 + - + +
116A ALA 4.0 3.4 - - - +
118A ALA* 1.3 70.7 - - - +
120A SER* 1.4 61.7 + - - +
122A CYS* 3.1 13.9 + - - +
123A VAL* 3.2 26.1 + - - +
133A THR* 2.7 36.8 + - - +
182A PHE* 3.7 14.8 - - + -
184A MSE 4.7 0.3 - - - +
103B PHE* 5.8 1.0 - - - -
110B ARG* 5.3 0.4 - - - +
111B GLY* 3.6 11.5 - - - +
112B HIS* 3.6 34.2 + - - +
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Residues in contact with SER 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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77A GLU 3.4 12.5 + - - -
78A PHE* 3.3 24.1 - - - -
79A ILE* 3.1 33.9 + - - +
116A ALA 3.0 19.8 + - - -
117A GLN 3.7 4.3 - - - -
119A ASN* 1.4 76.4 - - - +
121A LEU* 1.3 62.0 + - - +
123A VAL* 3.4 10.3 + - - +
124A ALA 3.2 17.0 + - - -
112B HIS* 4.0 5.2 - - - -
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Residues in contact with LEU 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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78A PHE* 3.8 5.6 - - - -
82A LEU* 3.7 15.3 - - + -
91A ALA* 3.8 11.7 - - + +
92A GLN 3.7 12.3 - - - -
93A SER* 3.7 23.3 - - - +
117A GLN 3.1 17.3 + - - +
118A ALA 3.4 6.1 - - - +
119A ASN 3.3 0.2 - - - -
120A SER* 1.3 75.8 - - - +
122A CYS* 1.3 56.4 + - - +
124A ALA* 3.4 2.8 + - - +
125A LEU* 2.9 29.6 + - - +
152A ALA* 3.4 39.0 - - + +
153A GLU 4.0 0.4 - - - +
154A ALA* 3.6 32.1 - - + +
168A VAL* 4.7 3.8 - - + -
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Residues in contact with CYS 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 ALA 3.2 18.1 + - - -
119A ASN 3.1 9.3 + - - +
121A LEU* 1.3 73.4 - - - +
123A VAL* 1.3 63.5 + - - +
125A LEU* 3.2 8.9 + - - +
126A ILE* 3.1 31.0 + - - +
154A ALA* 4.6 0.4 - - - -
166A VAL* 3.7 17.3 - - + -
168A VAL* 3.7 23.8 - - - -
182A PHE* 3.7 23.3 - - - -
184A MSE 3.7 26.0 - - + -
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Residues in contact with VAL 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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119A ASN* 3.2 27.1 + - - +
120A SER* 3.4 9.6 + - - +
122A CYS* 1.3 73.4 - - - +
124A ALA* 1.3 61.0 + - - +
126A ILE 3.2 18.2 - - - +
131A VAL* 4.3 25.7 - - + +
132A LEU* 6.2 0.4 - - - -
133A THR* 4.9 1.3 - - - +
184A MSE 3.9 15.3 - - + -
103B PHE* 4.1 34.1 - - + -
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Residues in contact with ALA 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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78A PHE* 3.8 20.4 - - + -
82A LEU* 4.0 24.0 - - + -
85A VAL* 4.2 14.8 - - + +
120A SER 3.2 13.3 + - - +
121A LEU 3.5 8.5 - - - +
123A VAL* 1.3 76.7 - - - +
125A LEU* 1.3 62.5 + - - +
126A ILE 3.6 3.5 + - - +
127A LYS* 5.4 1.7 - - - +
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Residues in contact with LEU 125 (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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85A VAL* 5.0 2.9 - - + -
86A ASN 3.5 11.7 - - - +
87A PRO* 3.8 5.4 - - - +
88A ASN 2.9 25.5 + - - -
89A VAL 3.6 6.3 - - - +
90A LYS 3.5 35.9 - - - +
91A ALA* 3.8 10.7 - - + +
121A LEU 2.9 18.2 + - - +
122A CYS* 3.2 5.8 + - - +
124A ALA* 1.3 77.0 - - - +
126A ILE* 1.3 60.0 + - + +
127A LYS* 3.4 1.6 + - - +
154A ALA* 3.8 24.2 - - + +
155A ARG 4.2 0.7 - - - +
156A VAL* 3.8 24.5 - - + +
166A VAL* 3.8 24.9 - - + -
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Residues in contact with ILE 126 (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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88A ASN* 3.4 6.1 - - - +
122A CYS 3.1 25.0 + - - +
123A VAL 3.2 14.2 - - - +
124A ALA 3.5 2.4 - - - +
125A LEU* 1.3 78.4 - - + +
127A LYS* 1.3 58.9 + - - +
128A GLN* 3.3 31.5 + - + +
131A VAL* 3.7 26.2 - - + +
156A VAL* 4.8 1.3 - - + -
164A TYR* 3.7 34.5 - - + -
166A VAL* 3.8 17.3 - - + -
184A MSE 3.7 33.9 - - + -
186A TYR* 4.5 1.8 - - + -
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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
------------------------------------------------------------
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