Contacts of the helix formed by residues 110 - 126 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77C GLU* 3.2 53.8 + - - +
119C ASN* 5.2 0.2 - - - +
99D SER 4.7 0.6 + - - -
100D ASP* 2.7 33.9 + - - +
101D SER* 3.0 13.6 + - - +
102D VAL 2.7 28.9 + - - -
103D PHE* 3.5 37.5 - - + +
109D ALA* 1.3 75.4 - - - +
111D GLY* 1.3 65.6 + - - +
112D HIS* 3.3 32.9 + - + -
113D VAL* 3.1 26.2 + - + +
114D LEU* 3.9 6.3 + - - +
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Residues in contact with GLY 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115C PHE* 4.2 3.1 - - - -
119C ASN* 3.7 19.2 - - - +
133C THR* 4.6 7.3 + - - -
103D PHE* 4.9 3.6 - - - -
109D ALA 3.8 1.8 + - - -
110D ARG* 1.3 72.4 - - - +
112D HIS* 1.3 59.7 + - - +
113D VAL 3.3 1.2 + - - -
114D LEU* 3.5 6.3 + - - -
115D PHE* 3.5 5.2 + - - +
140D PHE* 3.3 41.8 - - - -
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Residues in contact with HIS 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C GLU 4.8 1.3 - - - -
79C ILE* 4.2 10.4 - - + +
112C HIS* 5.2 2.3 - - - +
115C PHE* 3.7 18.6 - - + -
116C ALA* 3.5 33.0 + - + -
119C ASN* 3.5 18.1 + - + +
120C SER* 3.9 18.4 + - - -
73D ILE* 3.4 31.1 - - + +
103D PHE* 6.1 0.4 - + - -
110D ARG* 3.6 38.5 + - + +
111D GLY* 1.3 71.7 - - - +
113D VAL* 1.3 67.7 + - + +
114D LEU 3.5 0.2 - - - -
115D PHE* 3.9 1.7 - - - +
116D ALA* 2.9 31.2 + - - +
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Residues in contact with VAL 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D ILE* 4.9 16.8 - - + -
79D ILE* 4.2 1.0 - - - +
95D LEU* 3.9 23.4 - - + +
97D ILE* 4.2 8.5 - - + -
101D SER* 3.5 46.2 - - - +
109D ALA* 4.9 2.7 - - + -
110D ARG* 3.1 25.5 + - + +
112D HIS* 1.3 86.2 - - + +
114D LEU* 1.3 62.3 + - - +
116D ALA* 3.4 7.7 + - - +
117D GLN* 3.3 19.8 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D LEU* 5.3 1.1 - - + -
97D ILE* 5.3 2.2 - - + -
109D ALA* 4.2 18.6 - - + +
110D ARG 4.3 6.3 - - - +
111D GLY 3.5 6.0 + - - +
113D VAL* 1.3 75.5 - - + +
115D PHE* 1.3 64.1 + - - +
117D GLN* 3.6 10.2 + - - +
118D ALA* 3.2 21.7 + - - +
140D PHE* 4.1 15.9 - - + -
144D VAL* 3.8 36.3 - - + +
150D VAL* 3.7 35.2 - - + -
170D SER* 4.8 2.5 + - - -
177D VAL* 4.6 0.2 - - + -
178D PHE* 4.1 35.8 - - + -
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Residues in contact with PHE 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111C GLY 4.2 2.0 - - - -
112C HIS* 3.8 22.4 - - + -
115C PHE* 3.6 49.1 - + + -
138C ILE* 3.6 21.3 - - + -
140C PHE* 4.7 4.0 - + - -
111D GLY 3.5 6.2 + - - +
112D HIS 3.9 2.5 - - - +
113D VAL 3.4 0.4 - - - -
114D LEU* 1.3 74.1 - - - +
116D ALA* 1.4 57.7 + - - +
118D ALA* 3.2 5.7 + - - +
119D ASN* 2.8 45.1 + - + +
133D THR* 5.1 0.2 - - + -
136D SER* 3.4 26.9 - - - -
138D ILE* 3.7 30.3 - - + -
178D PHE* 4.3 5.1 - + - -
182D PHE* 3.5 20.2 - + - -
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Residues in contact with ALA 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112C HIS* 3.6 20.2 + - + -
73D ILE* 3.8 14.6 - - + -
79D ILE* 3.7 27.3 - - + +
112D HIS 2.9 19.1 + - - +
113D VAL 3.4 7.0 - - - +
115D PHE* 1.4 75.4 - - - +
117D GLN* 1.4 55.9 + - - +
119D ASN* 4.0 0.7 - - - +
120D SER* 3.0 35.2 + - - -
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Residues in contact with GLN 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79D ILE* 3.6 20.0 - - + +
80D GLY* 4.8 0.2 - - - -
93D SER* 3.1 35.6 + - - +
94D ILE 3.7 0.2 - - - -
95D LEU* 3.5 31.4 - - + +
113D VAL 3.3 9.5 + - - +
114D LEU* 3.8 11.0 - - - +
115D PHE 3.3 0.4 - - - -
116D ALA* 1.4 76.0 - - - +
118D ALA* 1.4 61.6 - - - +
120D SER* 3.6 1.7 + - - -
121D LEU* 3.1 23.6 + - - +
150D VAL* 3.1 47.1 + - - +
152D ALA* 3.5 14.6 - - + +
170D SER* 4.4 2.1 + - - -
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Residues in contact with ALA 118 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D LEU 3.2 12.3 + - - +
115D PHE 3.2 8.4 + - - +
117D GLN* 1.4 75.3 - - - +
119D ASN* 1.3 64.6 + - - +
121D LEU* 3.2 8.5 + - - +
122D CYS* 3.2 24.7 + - - -
152D ALA* 5.3 1.5 - - - +
168D VAL* 3.9 20.8 - - + +
170D SER* 5.3 0.7 - - - +
178D PHE* 3.7 20.9 - - + -
182D PHE* 3.7 20.0 - - + -
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Residues in contact with ASN 119 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 5.7 0.8 - - - -
110C ARG* 5.3 0.6 - - - +
111C GLY* 3.7 10.5 - - - +
112C HIS* 3.6 34.2 + - - +
115D PHE* 2.8 34.9 + - + +
116D ALA 4.0 2.9 - - - +
118D ALA* 1.3 71.5 - - - +
120D SER* 1.4 62.4 + - - +
122D CYS* 3.1 13.9 + - - +
123D VAL* 3.2 25.3 + - - +
133D THR* 2.7 36.7 + - - +
182D PHE* 3.7 16.2 - - + -
184D MSE 4.8 0.5 - - - +
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Residues in contact with SER 120 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C HIS* 4.0 5.4 - - - -
77D GLU 3.4 12.6 + - - -
78D PHE* 3.3 23.8 - - - -
79D ILE* 3.1 35.5 + - - +
116D ALA 3.0 18.6 + - - -
117D GLN 3.7 4.9 - - - -
119D ASN* 1.4 76.1 - - - +
121D LEU* 1.3 61.4 + - - +
123D VAL* 3.4 10.8 + - - +
124D ALA 3.2 17.3 + - - -
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Residues in contact with LEU 121 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 3.8 5.8 - - - -
82D LEU* 3.7 28.0 - - + -
91D ALA* 3.8 5.2 - - + +
92D GLN 3.8 10.3 - - - +
93D SER* 3.7 18.4 - - - +
117D GLN 3.1 15.2 + - - +
118D ALA 3.2 10.1 + - - +
120D SER* 1.3 74.2 - - - +
122D CYS* 1.3 56.0 + - - +
124D ALA* 3.4 2.9 + - - +
125D LEU* 2.9 30.2 + - - +
152D ALA* 3.4 39.5 - - + +
153D GLU 4.0 0.4 - - - +
154D ALA* 3.6 31.4 - - + +
168D VAL* 4.7 4.0 - - + -
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Residues in contact with CYS 122 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118D ALA 3.2 17.2 + - - -
119D ASN* 3.1 9.1 + - - +
121D LEU* 1.3 74.5 - - - +
123D VAL* 1.3 64.4 + - - +
125D LEU* 3.2 6.8 + - - +
126D ILE* 3.1 31.2 + - - +
154D ALA* 4.6 0.9 - - - -
166D VAL* 3.7 17.5 - - + -
168D VAL* 3.7 24.2 - - - -
182D PHE* 3.7 23.3 - - - -
184D MSE 3.8 24.9 - - + -
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Residues in contact with VAL 123 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103C PHE* 4.1 33.2 - - + -
119D ASN* 3.2 27.6 + - - +
120D SER* 3.4 8.0 + - - +
122D CYS* 1.3 74.4 - - - +
124D ALA* 1.3 61.2 + - - +
126D ILE* 3.2 18.4 - - - +
131D VAL* 4.3 27.0 - - + +
132D LEU* 6.2 0.2 - - - -
133D THR* 4.8 1.6 - - - +
184D MSE 3.8 16.2 - - + -
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Residues in contact with ALA 124 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78D PHE* 3.8 19.5 - - + -
82D LEU* 4.0 24.5 - - + -
85D VAL* 4.3 14.0 - - + +
120D SER 3.2 12.7 + - - +
121D LEU 3.5 8.5 - - - +
123D VAL* 1.3 77.0 - - - +
125D LEU* 1.3 62.7 + - - +
126D ILE 3.6 3.5 + - - +
127D LYS* 4.9 1.4 + - - +
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Residues in contact with LEU 125 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D VAL* 5.0 2.2 - - - -
86D ASN 3.5 11.9 - - - +
87D PRO* 3.7 4.9 - - - +
88D ASN 2.8 26.3 + - - -
89D VAL 3.6 6.5 - - - +
90D LYS 3.4 35.7 - - - +
91D ALA* 3.8 10.9 - - + +
121D LEU 2.9 17.3 + - - +
122D CYS* 3.2 5.1 + - - +
124D ALA* 1.3 77.9 - - - +
126D ILE* 1.3 60.0 + - + +
127D LYS* 3.4 1.2 + - - +
154D ALA* 3.7 35.9 - - + +
155D ARG 4.1 0.2 - - - +
156D VAL* 3.8 24.5 - - + +
166D VAL* 3.8 13.5 - - + -
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Residues in contact with ILE 126 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88D ASN* 3.4 7.0 - - - +
122D CYS 3.1 24.2 + - - +
123D VAL 3.2 14.6 - - - +
124D ALA 4.3 2.4 - - - +
125D LEU* 1.3 78.5 - - + +
127D LYS* 1.3 59.5 + - - +
128D GLN* 3.3 30.5 + - + +
131D VAL* 3.7 24.7 - - + +
156D VAL* 4.8 1.8 - - + -
164D TYR* 3.8 33.9 - - + -
166D VAL* 3.8 17.5 - - + -
184D MSE 3.7 34.5 - - + -
186D 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
------------------------------------------------------------
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