Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 4HI7
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 THR 158 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A SER 3.8 13.9 - - - +
85A LEU* 3.3 20.6 - - - +
87A PRO* 4.4 5.6 - - + -
96A VAL* 3.8 20.5 - - + +
153A ALA* 3.8 16.2 - - - +
156A GLN* 3.5 12.6 - - + +
157A LEU* 1.3 81.6 - - - +
159A ILE* 1.3 60.5 + - - +
160A ALA* 3.3 19.5 + - - +
161A ASP* 2.8 36.9 + - - +
162A PHE* 3.5 6.9 + - - -
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Residues in contact with ILE 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A THR* 4.1 11.9 - - + +
72A MET* 3.8 21.5 - - + +
73A ALA* 3.6 26.7 - - - +
76A VAL* 3.7 25.4 - - + -
85A LEU* 3.0 15.5 + - + +
86A TYR* 3.7 17.5 - - + -
96A VAL* 3.9 8.3 - - + -
100A MET* 3.6 30.7 - - + -
158A THR* 1.3 72.4 - - - +
160A ALA* 1.3 60.2 + - - +
162A PHE* 3.2 14.8 + - + +
163A SER* 2.9 27.9 + - - -
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Residues in contact with ALA 160 (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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96A VAL* 3.8 17.5 - - + +
99A ARG* 3.7 20.9 - - + -
100A MET* 3.9 11.7 - - + +
152A VAL* 3.7 17.5 - - + -
153A ALA* 4.0 3.1 - - + -
158A THR* 3.1 12.7 + - - +
159A ILE* 1.3 82.8 - - - +
161A ASP* 1.3 56.3 + - - +
163A SER* 3.7 1.4 - - - -
164A LEU* 3.0 33.3 + - - +
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Residues in contact with ASP 161 (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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151A TYR* 3.5 17.9 - - - +
152A VAL* 3.0 24.9 + - - +
153A ALA 4.9 0.3 + - - -
156A GLN 4.0 0.3 - - - +
157A LEU* 3.6 20.1 - - + -
158A THR* 2.8 36.0 + - - +
160A ALA* 1.3 73.3 - - - +
162A PHE* 1.3 62.0 + - - +
165A ILE* 2.8 35.8 + - - +
188A TRP* 2.9 33.4 + - - +
192A LEU* 4.3 4.3 - - + -
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Residues in contact with PHE 162 (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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17A ALA* 3.7 14.3 - - - +
20A LEU* 3.8 22.6 - - + +
21A THR* 3.3 35.7 - - - -
24A ALA* 3.9 12.1 - - + -
72A MET* 4.1 3.6 - - - -
85A LEU* 4.1 16.6 - - + -
157A LEU* 3.9 28.0 - - + -
158A THR 3.5 2.4 + - - -
159A ILE* 3.2 19.2 + - + +
161A ASP* 1.3 78.4 - - - +
163A SER* 1.3 63.6 + - - +
165A ILE* 3.4 8.5 - - + +
166A SER* 3.1 25.1 + - - -
192A LEU* 5.7 1.8 - - + -
195A LEU* 4.2 6.7 - - + -
197A TYR* 3.3 36.6 - + - -
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Residues in contact with SER 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A ALA* 4.0 11.3 - - - +
68A SER* 5.0 0.7 + - - -
69A HIS* 3.1 31.9 + - - -
72A MET* 3.9 12.0 - - - +
100A MET* 4.3 7.6 - - - -
103A GLU* 3.2 17.8 + - - +
159A ILE 2.9 17.2 + - - -
160A ALA 3.7 4.7 - - - -
161A ASP 3.3 0.2 - - - -
162A PHE* 1.3 76.5 - - - +
164A LEU* 1.3 62.2 + - - +
166A SER* 2.7 21.1 + - - -
167A SER* 3.4 8.1 + - - -
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Residues in contact with LEU 164 (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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99A ARG* 4.1 16.4 - - + +
102A PHE* 4.1 8.5 - - + -
103A GLU* 3.6 27.6 - - + -
107A VAL* 3.9 22.2 - - + -
142A VAL* 4.4 10.5 - - + -
145A PHE* 4.3 16.2 - - + -
152A VAL* 4.1 25.1 - - + -
160A ALA 3.0 19.4 + - - +
163A SER* 1.3 78.9 - - - +
165A ILE* 1.3 58.2 + - - +
167A SER* 3.4 2.1 + - - +
168A ILE* 2.9 36.4 + - + +
188A TRP* 3.8 17.3 - - + -
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Residues in contact with ILE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LEU* 3.8 22.4 - - + -
161A ASP 2.8 26.2 + - - +
162A PHE* 3.4 8.5 - - + +
164A LEU* 1.3 72.6 - - - +
166A SER* 1.3 63.9 + - - +
168A ILE* 4.5 0.9 - - + +
169A SER* 2.7 42.1 + - - +
188A TRP* 3.6 12.9 - - + -
189A ILE* 3.9 34.8 - - + -
192A LEU* 3.5 23.6 - - + -
198A TYR* 3.4 31.9 - - + +
201A ASN* 4.2 1.8 - - - +
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Residues in contact with SER 166 (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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13A PRO* 3.2 34.6 + - - +
14A PRO* 4.6 1.2 - - - +
16A ARG* 3.1 9.4 + - - -
17A ALA* 3.7 15.3 - - - +
20A LEU* 5.4 0.4 - - - -
103A GLU* 4.4 2.9 + - - -
162A PHE 3.1 15.7 + - - -
163A SER 2.7 19.4 + - - -
165A ILE* 1.3 77.8 - - - +
167A SER* 1.3 56.6 + - - +
169A SER* 3.2 4.0 + - - -
170A SER* 2.8 21.7 + - - -
201A ASN* 3.6 17.5 - - - -
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Residues in contact with SER 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PRO* 4.2 4.3 - - - -
103A GLU* 2.6 30.7 + - - +
107A VAL* 3.4 21.2 - - - +
108A PHE* 4.9 2.9 - - - -
112A LEU* 3.4 26.1 - - - +
163A SER 3.4 1.9 + - - -
164A LEU* 3.4 7.3 + - - -
165A ILE 3.2 0.2 - - - -
166A SER* 1.3 80.5 + - - +
168A ILE* 1.3 60.1 + - - +
169A SER 3.3 0.2 - - - -
170A SER* 2.9 4.3 + - - -
171A LEU* 2.8 28.1 + - - +
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Residues in contact with ILE 168 (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 VAL* 4.7 7.4 - - + -
138A ALA* 5.3 2.5 - - + -
139A TYR* 3.6 36.3 + - + -
142A VAL* 4.7 14.8 - - + -
164A LEU* 2.9 34.9 + - + +
165A ILE* 4.3 1.8 - - + +
167A SER* 1.3 72.1 - - - +
169A SER* 1.3 62.3 + - - +
171A LEU* 3.1 24.7 + - + +
172A VAL* 3.2 15.3 + - + +
177A VAL* 4.6 5.2 - - + -
185A LEU* 4.6 9.6 - - + -
188A TRP* 4.4 17.0 - - + -
189A ILE* 4.1 26.9 - - + -
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Residues in contact with SER 169 (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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16A ARG* 3.4 5.7 + - - -
165A ILE* 2.7 27.4 + - - +
166A SER 3.2 8.5 + - - -
168A ILE* 1.3 76.1 - - - +
170A SER* 1.3 57.0 + - - +
172A VAL* 3.3 22.5 - - - +
189A ILE* 6.2 2.9 - - - -
198A TYR* 4.1 8.7 - - - -
201A ASN* 3.0 25.3 + - - -
205A ALA* 3.7 17.4 - - - +
209A VAL* 4.3 5.9 - - - +
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Residues in contact with SER 170 (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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13A PRO* 3.4 4.3 - - - +
16A ARG* 2.9 23.2 + - - -
112A LEU* 3.6 16.4 - - - -
166A SER 2.8 19.4 + - - -
167A SER 2.9 8.6 + - - -
169A SER* 1.3 77.3 + - - +
171A LEU* 1.3 61.3 + - - +
172A VAL 3.1 2.5 - - - -
173A ALA* 3.0 29.8 + - - +
174A PHE* 4.3 0.3 - - - -
205A ALA* 5.4 0.2 - - - -
208A PHE* 3.4 29.3 - - - -
209A VAL* 5.3 0.4 - - - -
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Residues in contact with LEU 171 (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 VAL* 3.8 29.6 - - + +
111A ALA* 3.9 9.0 - - + +
112A LEU* 3.8 33.4 - - + -
135A ILE* 3.8 32.0 - - + +
138A ALA* 5.0 4.5 - - + -
139A TYR* 3.4 22.3 + - + +
167A SER 2.8 15.9 + - - +
168A ILE* 3.1 17.4 + - + +
170A SER* 1.3 73.8 - - - +
172A VAL* 1.3 57.0 + - - +
173A ALA 3.0 5.8 - - - -
174A PHE* 2.8 30.1 + - + +
175A VAL* 3.0 10.4 + - - +
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Residues in contact with VAL 172 (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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139A TYR* 4.0 2.0 - - - +
168A ILE* 3.2 13.2 + - + +
169A SER* 3.3 26.2 - - - +
171A LEU* 1.3 73.9 - - - +
173A ALA* 1.3 67.0 + - - +
174A PHE 3.0 0.6 + - - -
175A VAL 3.3 8.3 - - - +
176A PRO* 3.5 24.9 - - + +
177A VAL* 3.9 34.5 - - + +
189A ILE* 5.4 3.6 - - + -
209A VAL* 4.5 8.7 - - + -
213A LYS* 5.1 1.2 + - - -
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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