Contacts of the helix formed by residues 110 - 126 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74A GLU 4.6 1.4 + - - -
76A GLN 3.3 19.8 + - - +
77A GLU* 3.3 36.5 - - - +
119A ASN* 5.3 0.7 - - - +
100B ASP 2.9 26.3 + - - -
101B SER* 3.0 20.7 + - - +
102B VAL 2.7 25.6 + - - -
103B PHE* 3.6 47.9 - - + +
104B HIS* 3.7 11.9 + - - -
109B ALA* 1.3 74.0 - - - +
111B GLY* 1.3 66.6 + - - +
112B HIS* 3.3 28.9 - - + -
113B VAL* 3.1 21.9 + - + +
114B LEU* 3.9 6.1 + - - +
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Residues in contact with GLY 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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115A PHE* 4.3 2.7 - - - -
119A ASN* 3.6 18.6 - - - +
133A THR* 4.5 7.1 + - - +
103B PHE* 5.0 3.4 - - - -
109B ALA 3.8 1.6 + - - -
110B ARG* 1.3 72.5 - - - +
112B HIS* 1.3 61.0 + - - +
113B VAL 3.3 0.9 + - - -
114B LEU* 3.5 6.8 + - - -
115B PHE* 3.5 4.9 + - - +
140B PHE* 3.3 41.4 - - - -
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Residues in contact with HIS 112 (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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73A ILE* 3.6 20.4 + - + -
76A GLN 3.1 21.0 + - - -
77A GLU 3.7 11.2 - - - -
79A ILE* 3.4 24.2 - - + +
112A HIS* 5.2 1.3 - - - +
115A PHE* 3.9 16.8 - - + -
116A ALA* 3.7 27.4 + - + -
119A ASN* 3.6 17.7 + - - +
120A SER* 4.0 8.0 + - - -
110B ARG* 3.6 26.7 - - + +
111B GLY* 1.3 71.9 - - - +
113B VAL* 1.3 69.3 + - + +
114B LEU 3.4 0.2 - - - -
115B PHE* 3.9 1.8 - - - +
116B ALA* 2.9 32.2 + - - +
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Residues in contact with VAL 113 (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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74A GLU* 3.3 42.1 - - + +
95B LEU* 3.9 20.3 - - + +
97B ILE* 4.1 9.4 - - + -
101B SER* 3.5 35.4 - - - +
109B ALA* 4.9 3.4 - - + -
110B ARG* 3.1 25.7 + - + +
112B HIS* 1.3 83.8 - - + +
114B LEU* 1.3 62.7 + - + +
116B ALA* 3.4 4.2 + - - +
117B GLN* 3.3 19.9 + - - +
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Residues in contact with LEU 114 (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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95B LEU* 5.3 1.6 - - + -
97B ILE* 5.3 1.6 - - + -
109B ALA* 4.2 17.5 - - + +
110B ARG 4.3 6.7 - - - +
111B GLY 3.5 5.6 + - - +
112B HIS 3.4 0.4 - - - -
113B VAL* 1.3 76.3 - - + +
115B PHE* 1.3 63.9 + - - +
117B GLN* 3.6 11.1 + - - +
118B ALA* 3.2 22.7 + - - +
140B PHE* 4.2 15.7 - - + -
144B VAL* 3.8 36.3 - - + +
150B VAL* 3.7 35.2 - - + -
170B SER* 4.8 2.3 + - - -
177B VAL* 4.6 0.7 - - + +
178B PHE* 4.1 34.6 - - + -
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Residues in contact with PHE 115 (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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111A GLY 4.2 0.9 - - - -
112A HIS* 3.7 30.3 - - + -
115A PHE* 3.6 43.3 - + + -
138A ILE* 3.6 22.4 - - + -
140A PHE* 4.7 3.4 - + - -
111B GLY 3.5 6.1 + - - +
112B HIS 3.9 3.4 - - - +
113B VAL 3.4 0.4 - - - -
114B LEU* 1.3 74.1 - - - +
116B ALA* 1.3 57.4 + - - +
118B ALA* 3.2 5.4 + - - +
119B ASN* 2.8 44.7 + - + +
136B SER* 3.4 26.7 - - - -
138B ILE* 3.7 30.1 - - + -
178B PHE* 4.3 4.4 - - - -
182B PHE* 3.5 21.1 - + - -
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Residues in contact with ALA 116 (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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73A ILE* 4.0 12.6 - - + -
74A GLU* 4.6 0.7 - - + -
112A HIS* 3.6 23.2 + - + -
79B ILE* 3.8 24.9 - - + -
112B HIS 2.9 19.3 + - - +
113B VAL* 3.5 7.9 - - - +
115B PHE* 1.3 76.9 - - - +
117B GLN* 1.3 56.1 + - - +
119B ASN* 4.0 1.0 - - - +
120B SER* 3.0 34.7 + - - -
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Residues in contact with GLN 117 (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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79B ILE* 3.7 20.9 - - + +
80B GLY* 4.9 0.2 - - - -
93B SER* 3.1 35.1 + - - +
94B ILE 3.5 9.7 - - - -
95B LEU* 3.6 23.4 - - + +
113B VAL 3.3 9.5 + - - +
114B LEU* 3.8 10.9 - - - +
115B PHE 3.3 0.2 - - - -
116B ALA* 1.3 76.7 - - - +
118B ALA* 1.4 58.1 + - - +
120B SER* 3.5 2.1 + - - -
121B LEU* 3.1 28.6 + - - +
150B VAL* 3.1 47.3 + - - +
152B ALA* 3.5 13.7 - - + +
170B SER* 4.4 1.9 + - - -
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Residues in contact with ALA 118 (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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114B LEU 3.2 11.4 + - - +
115B PHE 3.2 8.5 + - - +
117B GLN* 1.4 75.7 - - - +
119B ASN* 1.3 64.5 + - - +
121B LEU* 3.3 7.9 + - - +
122B CYS* 3.2 25.5 + - - -
152B ALA* 5.3 1.8 - - - +
168B VAL* 3.9 19.6 - - + +
170B SER* 5.3 1.1 - - - +
178B PHE* 3.7 21.3 - - + -
182B PHE* 3.7 19.3 - - + -
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Residues in contact with ASN 119 (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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103A PHE* 5.6 0.9 - - - -
110A ARG* 5.2 0.5 - - - +
111A GLY* 3.7 9.2 + - - -
112A HIS* 3.4 32.7 + - + +
115B PHE* 2.8 34.0 + - + +
116B ALA 4.0 3.1 - - - +
118B ALA* 1.3 70.6 - - - +
120B SER* 1.4 62.9 + - - +
122B CYS* 3.1 14.3 + - - +
123B VAL* 3.2 23.6 + - - +
133B THR* 2.7 41.8 + - - +
182B PHE* 3.7 15.9 - - + -
184B MSE 4.8 0.6 - - - -
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Residues in contact with SER 120 (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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112A HIS* 3.9 12.3 + - - -
77B GLU 4.3 1.4 + - - -
78B PHE* 3.3 26.4 - - - -
79B ILE* 3.1 36.6 + - - +
116B ALA 3.0 19.5 + - - -
117B GLN 3.7 4.7 - - - -
119B ASN* 1.4 76.0 + - - +
121B LEU* 1.4 62.3 + - - +
123B VAL* 3.4 9.9 + - - +
124B ALA 3.2 17.5 + - - -
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Residues in contact with LEU 121 (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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78B PHE* 3.9 5.6 - - - -
82B LEU* 3.7 17.5 - - + -
91B ALA* 3.7 11.7 - - + +
92B GLN 3.7 3.1 - - - -
93B SER* 3.6 29.2 - - - +
117B GLN 3.1 17.1 + - - +
118B ALA 3.4 6.1 - - - +
119B ASN 3.3 0.2 - - - -
120B SER* 1.4 74.5 - - - +
122B CYS* 1.4 57.2 + - - +
124B ALA* 3.4 2.9 + - - +
125B LEU* 2.9 29.7 + - - +
152B ALA* 3.4 39.0 - - + +
153B GLU 4.0 0.4 - - - +
154B ALA* 3.6 31.6 - - + +
168B VAL* 4.7 4.7 - - + -
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Residues in contact with CYS 122 (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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118B ALA 3.2 18.5 + - - -
119B ASN* 3.1 9.9 + - - +
121B LEU* 1.4 73.1 - - - +
123B VAL* 1.3 65.2 + - - +
125B LEU* 3.2 8.1 + - - +
126B ILE* 3.1 30.8 + - - +
154B ALA* 4.6 0.9 - - - -
166B VAL* 3.8 15.7 - - + -
168B VAL* 3.7 24.5 - - - -
182B PHE* 3.7 23.1 - - - -
184B MSE 3.8 25.1 - - + -
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Residues in contact with VAL 123 (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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103A PHE* 4.2 35.7 - - + -
119B ASN* 3.2 25.0 + - - +
120B SER* 3.4 8.9 + - - +
122B CYS* 1.3 74.1 - - - +
124B ALA* 1.3 61.0 + - - +
126B ILE* 3.2 18.4 - - - +
131B VAL* 4.3 27.0 - - + +
132B LEU* 6.3 0.2 - - - -
133B THR* 4.9 1.6 - - - +
184B MSE 3.8 15.7 - - + -
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Residues in contact with ALA 124 (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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78B PHE* 3.8 20.2 - - + -
82B LEU* 4.0 23.3 - - + +
85B VAL* 4.3 15.2 - - + +
120B SER 3.2 13.2 + - - +
121B LEU* 3.5 8.5 - - - +
123B VAL* 1.3 76.4 - - - +
125B LEU* 1.3 63.4 + - - +
126B ILE 4.3 3.1 - - - +
127B LYS* 4.9 1.7 + - - +
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Residues in contact with LEU 125 (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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85B VAL* 5.0 2.2 - - - -
86B ASN 3.6 11.9 - - - +
87B PRO* 3.8 5.5 - - - +
88B ASN 2.9 25.3 + - - -
89B VAL 3.6 6.5 - - - +
90B LYS 3.5 36.1 - - - +
91B ALA* 3.8 10.1 - - + +
121B LEU 2.9 17.1 + - - +
122B CYS* 3.2 6.0 + - - +
124B ALA* 1.3 77.4 - - - +
126B ILE* 1.3 60.2 + - + +
127B LYS* 3.4 1.2 + - - +
154B ALA* 3.8 24.7 - - + +
155B ARG 4.2 0.2 - - - +
156B VAL* 3.8 25.1 - - + +
166B VAL* 3.8 24.5 - - + -
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Residues in contact with ILE 126 (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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88B ASN* 3.4 7.0 - - - +
122B CYS 3.1 25.0 + - - +
123B VAL 3.2 14.2 - - - +
124B ALA 4.3 2.2 - - - +
125B LEU* 1.3 78.1 - - + +
127B LYS* 1.3 59.8 + - - +
128B GLN* 3.3 31.7 + - + +
131B VAL* 3.7 24.3 - - + +
156B VAL* 4.8 1.1 - - + -
164B TYR* 3.8 34.3 - - + -
166B VAL* 3.8 17.3 - - + -
184B MSE 3.7 34.1 - - + -
186B TYR* 4.5 2.0 - - + -
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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