Contacts of the helix formed by residues 142 - 161 (chain A) in PDB entry 1H13
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 ALA 142 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A THR* 3.8 11.0 + - - +
78A GLU* 4.1 23.6 - - + +
122A TYR 4.3 0.4 + - - -
124A TRP* 3.7 27.1 - - + +
141A PRO* 1.3 71.0 - - - +
143A PRO* 1.3 57.5 - - - +
144A ASP* 3.2 3.6 - - - +
145A GLY* 2.8 29.8 + - - -
146A GLU* 3.2 5.9 + - - +
203A TYR* 4.2 8.3 - - - +
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Residues in contact with PRO 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141A PRO* 3.5 10.8 - - + +
142A ALA* 1.3 86.2 - - - +
144A ASP* 1.3 61.1 + - - +
145A GLY 3.1 0.2 - - - -
146A GLU* 3.3 14.8 + - - +
147A GLU* 3.2 24.1 + - - +
183A LEU* 4.0 27.7 - - + +
189A ILE* 4.0 18.0 - - + +
190A ARG* 3.3 26.0 - - + +
191A PHE 3.7 17.5 - - - +
192A SER* 5.4 0.9 - - - -
203A TYR* 3.7 11.4 - - + +
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Residues in contact with ASP 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A GLU* 2.4 34.6 - - - +
82A TRP* 4.2 5.6 + - - -
142A ALA 3.6 2.4 - - - +
143A PRO* 1.3 71.5 - - - +
145A GLY* 1.3 61.6 + - - +
147A GLU* 3.4 20.4 - - - +
148A TYR* 3.0 43.1 + - + -
202A SER 4.5 3.2 - - - +
203A TYR* 3.3 30.8 - - + -
205A ILE* 5.6 0.9 - - + -
284A ARG* 2.9 28.8 + - - -
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Residues in contact with GLY 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 4.0 19.1 - - - -
78A GLU* 4.3 3.0 - - - +
81A SER* 3.4 17.0 - - - -
142A ALA 2.8 19.8 + - - -
144A ASP* 1.3 72.5 + - - +
146A GLU* 1.3 59.0 + - - -
148A TYR 3.1 2.1 + - - -
149A PHE* 2.8 37.7 + - - -
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Residues in contact with GLU 146 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A THR* 4.9 1.2 + - - -
121A VAL* 3.5 4.5 - - - +
122A TYR* 2.7 43.9 + - + +
141A PRO* 3.5 14.4 - - - +
142A ALA 3.2 19.6 + - - +
143A PRO* 3.3 10.2 + - - +
145A GLY* 1.3 74.8 - - - +
147A GLU* 1.3 62.9 + - - +
149A PHE* 3.2 6.9 + - - -
150A ALA* 2.9 22.0 + - - +
175A MET* 3.4 27.0 - - - +
178A THR* 4.9 4.3 - - + -
179A ILE* 3.8 13.0 - - + -
183A LEU* 3.6 24.0 - - + -
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Residues in contact with GLU 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A PRO 3.2 12.2 + - - +
144A ASP* 3.4 21.7 - - - +
146A GLU* 1.3 76.3 - - - +
148A TYR* 1.3 59.6 + - + +
150A ALA 3.4 0.3 + - - -
151A PHE* 3.0 26.7 + - - +
179A ILE* 3.9 15.3 - - + -
184A MET* 4.9 0.2 - - - +
189A ILE* 3.5 28.2 - - + +
203A TYR* 2.6 23.5 - - - +
205A ILE* 4.8 4.3 - - + +
208A PHE* 4.3 12.1 - - + -
209A TYR* 2.7 38.0 + - + -
212A PHE* 3.6 12.8 - - + -
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Residues in contact with TYR 148 (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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81A SER* 3.2 25.4 - - - +
82A TRP* 3.3 36.9 + + - -
85A THR* 3.4 29.4 + - + +
144A ASP* 3.0 31.4 + - + +
147A GLU* 1.3 72.4 - - + +
149A PHE* 1.3 61.2 + - - +
151A PHE* 3.6 5.2 - + - +
152A ALA* 2.8 32.6 + - - +
205A ILE* 3.5 31.4 - - + +
208A PHE* 3.7 24.9 - + - -
284A ARG* 6.0 2.5 - - - -
287A MET* 4.6 8.0 - - - +
288A ASN* 4.3 8.1 + - - -
291A LEU* 4.8 6.4 - - - +
388A LEU* 4.5 13.3 - - + +
392A HIS* 5.5 1.9 + - - -
397A PHE* 4.8 4.3 - + - -
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Residues in contact with PHE 149 (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 THR* 4.0 18.2 - - - -
80A GLN* 4.1 2.9 - - + -
81A SER* 3.5 25.4 - - - -
84A MET* 3.6 28.3 - - + -
100A TRP* 4.2 3.1 - + - -
103A ALA* 3.8 11.0 - - + -
107A GLN* 3.6 21.5 - - - -
122A TYR* 3.7 28.7 - + + -
145A GLY 2.8 32.4 + - - -
146A GLU* 3.6 9.6 - - - +
148A TYR* 1.3 72.0 - - - +
150A ALA* 1.3 63.8 + - - +
152A ALA* 3.3 3.9 + - - +
153A LEU* 2.9 33.9 + - + +
175A MET* 3.7 25.6 - - + -
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Residues in contact with ALA 150 (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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146A GLU 2.9 16.7 + - - +
147A GLU 3.7 4.5 - - - +
149A PHE* 1.3 76.0 - - - +
151A PHE* 1.3 63.8 + - - +
153A LEU* 3.9 4.1 - - - +
154A LEU* 3.0 28.9 + - - +
172A ALA* 4.0 3.3 - - - +
175A MET* 3.8 21.0 - - + +
176A LEU* 3.6 33.0 - - + -
179A ILE* 4.2 2.7 - - + -
212A PHE* 4.0 5.2 - - + -
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Residues in contact with PHE 151 (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 THR* 4.0 14.8 - - + -
89A MET* 3.5 28.0 - - + -
147A GLU 3.0 17.9 + - - +
148A TYR 3.6 2.7 - - - +
150A ALA* 1.3 77.9 - - - +
152A ALA* 1.3 64.8 + - - +
154A LEU* 3.3 2.3 + - - +
155A ASN* 2.8 44.1 + - - +
208A PHE* 3.6 38.8 - + + -
211A TYR* 3.6 22.9 - + - -
212A PHE* 3.7 8.7 - - + -
397A PHE* 3.7 15.7 - + - -
399A PHE* 3.4 41.1 - + - -
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Residues in contact with ALA 152 (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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84A MET* 4.1 9.2 - - + -
85A THR* 3.6 26.9 - - - +
88A VAL* 4.2 7.4 - - - +
96A PHE* 3.7 22.6 - - + -
148A TYR 2.8 22.2 + - - +
149A PHE 3.8 2.5 - - - +
151A PHE* 1.3 78.8 - - - +
153A LEU* 1.3 56.9 + - - +
155A ASN* 3.3 4.2 + - - +
156A ALA* 2.9 28.1 + - - +
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Residues in contact with LEU 153 (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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84A MET* 4.1 4.9 - - + -
96A PHE* 3.9 16.4 - - + -
100A TRP* 3.6 62.4 - - + +
149A PHE* 2.9 26.8 + - + +
150A ALA 4.6 0.2 - - - +
152A ALA* 1.3 72.7 - - - +
154A LEU* 1.3 66.8 + - - +
156A ALA* 3.2 0.4 + - - -
157A SER* 2.9 21.1 + - - -
168A TYR* 3.5 22.6 - - + +
171A ASP* 4.1 22.2 - - + +
172A ALA* 3.7 17.3 - - + +
175A MET* 4.5 3.1 - - + -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A ALA 3.0 18.9 + - - +
151A PHE 3.3 0.4 + - - +
153A LEU* 1.3 76.8 - - - +
155A ASN* 1.3 62.1 + - - +
157A SER* 3.4 3.1 + - - -
158A ALA* 3.1 11.4 + - - +
169A TYR* 3.8 29.2 - - + -
172A ALA* 3.6 20.2 - - + -
173A ILE* 4.6 5.8 - - + -
176A LEU* 4.4 9.2 - - + -
211A TYR* 3.4 26.2 + - + +
212A PHE* 3.6 33.7 - - + -
215A ASN* 4.0 23.1 - - + +
402A ASN* 3.0 20.2 - - - +
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Residues in contact with ASN 155 (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 VAL* 3.8 18.6 - - + -
89A MET* 4.5 4.7 - - - -
151A PHE* 2.8 46.2 + - - +
152A ALA 3.6 7.0 - - - +
154A LEU* 1.3 73.9 - - - +
156A ALA* 1.3 64.4 + - - +
158A ALA* 3.1 1.6 + - - +
159A ARG* 2.9 28.2 + - - +
211A TYR* 3.2 12.0 + - - -
398A LYS 3.8 4.2 + - - -
399A PHE* 3.8 1.8 - - - +
400A TYR* 2.8 49.2 - - + +
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Residues in contact with ALA 156 (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 VAL* 3.6 8.9 - - - +
96A PHE* 3.6 22.2 - - + -
152A ALA 2.9 16.7 + - - +
153A LEU 3.6 5.2 - - - +
155A ASN* 1.3 72.7 - - - +
157A SER* 1.3 61.1 + - - +
160A TRP* 2.8 56.1 + - + +
161A GLY 3.8 0.2 + - - -
168A TYR* 3.6 14.2 - - + -
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Residues in contact with SER 157 (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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153A LEU 2.9 12.5 + - - -
154A LEU 3.4 7.6 - - - -
156A ALA* 1.3 76.5 - - - +
158A ALA* 1.3 57.3 + - - +
161A GLY* 2.9 26.0 + - - -
162A ASN* 2.9 37.6 + - - -
168A TYR* 3.6 4.1 - - - +
169A TYR* 3.4 19.6 - - - +
402A ASN* 2.7 25.9 + - - -
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Residues in contact with ALA 158 (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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154A LEU 3.1 7.3 + - - +
155A ASN 3.1 7.2 + - - +
157A SER* 1.3 80.3 - - - +
159A ARG* 1.3 62.4 + - - +
161A GLY 4.9 0.2 + - - -
400A TYR* 3.2 33.9 - - + +
401A ASN 3.4 21.6 - - - +
402A ASN* 3.2 10.3 - - - +
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Residues in contact with ARG 159 (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 VAL* 2.9 34.8 + - - -
89A MET 3.4 16.4 + - - -
90A LEU 4.3 0.2 - - - -
91A ASN* 3.3 36.7 + - - +
155A ASN 2.9 19.3 + - - +
156A ALA 4.2 0.2 - - - +
158A ALA* 1.3 78.7 - - - +
160A TRP* 1.3 79.8 + - + +
161A GLY 3.8 0.2 - - - -
400A TYR* 3.5 54.6 + - + -
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Residues in contact with TRP 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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88A VAL* 3.8 24.0 - - + -
91A ASN* 2.8 27.3 + - - -
92A LYS 4.0 11.2 - - - -
93A GLN* 3.7 54.4 + - + +
96A PHE* 3.5 42.8 - + + -
156A ALA* 2.8 34.5 + - + +
159A ARG* 1.3 92.9 - - + +
161A GLY* 1.3 64.1 + - - +
168A TYR* 3.6 17.9 - - + -
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Residues in contact with GLY 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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156A ALA 3.8 0.2 + - - -
157A SER 2.9 17.5 + - - -
158A ALA 4.7 0.4 + - - -
159A ARG 3.8 0.4 - - - -
160A TRP* 1.3 82.8 - - - +
162A ASN* 1.3 67.3 + - - -
163A SER 3.7 2.4 + - - -
164A GLY 5.2 1.2 + - - -
168A TYR* 3.2 24.8 - - - -
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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
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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