Contacts of the helix formed by residues 161 - 177 (chain A) in PDB entry 1Y2C
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 ASN 161 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A TYR* 3.4 17.7 - - - -
154A HIS 3.5 17.3 - - - +
157A VAL 2.9 25.6 + - - +
158A ALA 3.0 22.2 + - - -
159A TYR 2.8 9.7 + - - +
160A HIS* 1.3 74.0 - - - +
162A ASN* 1.3 67.8 + - - +
163A ILE* 2.9 30.4 + - - +
164A HIS* 3.2 10.4 + - - +
165A ALA 3.1 17.2 + - - -
332A TRP* 5.1 1.0 - - - -
335A ARG* 3.6 13.5 - - - +
515A EDO 3.8 14.1 - - - -
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Residues in contact with ASN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN* 3.0 31.1 + - - +
117A PRO* 3.4 7.6 - - - +
118A LEU* 4.0 5.7 - - + +
150A GLU* 2.9 34.7 + - + +
153A TYR* 3.5 17.4 - - + +
154A HIS 5.3 0.2 - - - +
161A ASN* 1.3 71.0 - - - +
163A ILE* 1.3 61.5 + - - -
165A ALA* 3.4 5.7 + - - +
166A ALA* 3.0 28.9 + - - +
507A EDO 3.2 21.8 + - - +
515A EDO 2.8 26.9 + - - -
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Residues in contact with ILE 163 (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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106A VAL* 4.0 25.0 - - + +
107A PHE* 4.0 17.3 - - + -
110A ALA* 4.1 20.9 - - + -
117A PRO* 4.2 8.1 - - + -
161A ASN* 2.9 10.7 + - - +
162A ASN* 1.3 76.5 - - - +
164A HIS* 1.3 61.4 + - - +
166A ALA* 3.3 2.3 + - - +
167A ASP* 2.9 27.2 + - - +
332A TRP* 3.8 18.4 - - + -
335A ARG* 4.0 23.6 - - - +
515A EDO 3.4 32.5 - - - +
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Residues in contact with HIS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TYR* 3.2 55.4 + + - +
160A HIS* 4.0 8.3 - + - -
161A ASN* 3.2 9.0 + - - +
163A ILE* 1.3 75.9 - - - +
165A ALA* 1.3 59.3 + - - +
167A ASP* 3.2 7.3 + - - +
168A VAL* 2.9 43.7 + - + +
200A HIS* 3.2 9.1 + + - -
201A ASP* 3.1 20.9 - - + -
318A ASP* 3.1 14.5 + - - -
321A ASN* 5.5 0.9 - - - -
332A TRP* 3.7 16.4 - - + -
1001A ZN 2.2 30.2 - - - -
1003A 3DE 6.3 0.4 - + - -
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Residues in contact with ALA 165 (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 LEU* 4.0 10.1 - - + -
153A TYR* 3.4 42.4 - - + +
161A ASN 3.1 6.2 + - - +
162A ASN 3.6 7.9 - - - +
163A ILE 3.3 0.2 - - - -
164A HIS* 1.3 76.9 - - - +
166A ALA* 1.3 57.9 + - - +
168A VAL* 3.2 2.8 + - - +
169A VAL* 2.9 33.3 + - - +
197A SER 4.1 5.6 - - - +
198A ALA 3.8 9.6 - - - +
200A HIS* 4.6 7.2 - - - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A VAL* 4.2 3.4 - - + -
117A PRO* 3.7 18.2 - - + +
118A LEU* 3.7 31.8 - - - +
121A ILE* 3.9 14.3 - - + +
162A ASN 3.0 17.5 + - - +
163A ILE 3.6 5.4 - - - +
164A HIS 3.3 0.2 - - - -
165A ALA* 1.3 75.5 - - - +
167A ASP* 1.3 57.3 + - - +
169A VAL* 3.4 4.0 + - - +
170A GLN* 3.0 30.0 + - - +
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Residues in contact with ASP 167 (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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106A VAL* 4.2 16.2 - - + +
163A ILE 2.9 17.1 + - - +
164A HIS* 3.2 8.8 + - - +
166A ALA* 1.3 74.0 - - - +
168A VAL* 1.3 61.4 + - - +
170A GLN* 3.4 7.5 + - - +
171A SER* 2.8 34.3 + - - -
317A ALA 5.2 0.3 - - - +
320A SER* 4.4 3.0 + - - -
321A ASN* 3.4 25.5 + - - -
324A LYS* 3.0 27.9 + - - -
332A TRP* 3.6 24.9 + - + -
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Residues in contact with VAL 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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164A HIS* 2.9 47.2 + - + +
165A ALA 3.9 2.2 - - - +
167A ASP* 1.3 75.1 - - - +
169A VAL* 1.3 61.1 + - - +
171A SER* 3.3 5.7 + - - -
172A THR* 2.9 34.1 + - - -
197A SER* 4.0 16.4 - - - +
200A HIS* 3.6 25.4 - - + +
314A VAL* 4.4 8.1 - - + +
317A ALA* 3.9 20.2 - - + +
318A ASP* 3.9 18.2 - - + +
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Residues in contact with VAL 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A LEU* 4.0 6.5 - - + -
121A ILE* 4.3 4.7 - - + -
122A MET* 3.5 26.2 - - + -
125A ILE* 3.7 20.0 - - + -
165A ALA 2.9 17.4 + - - +
166A ALA* 3.5 8.7 - - - +
168A VAL* 1.3 76.5 - - - +
170A GLN* 1.3 59.5 + - - +
172A THR* 3.3 2.6 + - - -
173A HIS* 2.9 26.5 + - - +
194A ILE* 4.0 10.2 - - + +
197A SER* 3.7 9.4 - - - -
198A ALA* 3.4 41.1 - - + +
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Residues in contact with GLN 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A VAL* 2.9 38.5 + - + +
101A LYS 2.8 27.5 + - - +
102A TRP* 5.4 1.2 - - - -
103A GLY 5.1 1.0 + - - -
104A LEU* 3.7 38.0 + - + +
121A ILE* 4.0 9.2 - - + -
125A ILE* 4.0 8.7 - - + -
166A ALA 3.0 17.8 + - - +
167A ASP* 4.0 7.1 - - - +
169A VAL* 1.3 76.7 - - - +
171A SER* 1.3 64.9 + - - +
173A HIS* 3.4 2.1 + - - +
174A VAL* 3.0 34.7 + - - +
324A LYS* 4.7 6.6 + - - -
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Residues in contact with SER 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A TRP* 3.6 20.9 - - - -
167A ASP* 2.8 22.0 + - - -
168A VAL* 3.7 4.3 - - - -
170A GLN* 1.3 77.8 + - - +
172A THR* 1.3 63.7 + - - +
174A VAL 3.2 1.4 + - - -
175A LEU* 3.0 27.7 + - - +
317A ALA* 3.8 17.5 - - - -
320A SER* 3.6 9.5 + - - -
324A LYS* 2.9 27.9 + - - -
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Residues in contact with THR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A VAL* 2.9 16.7 + - - +
169A VAL 3.6 3.6 - - - -
171A SER* 1.3 76.6 - - - +
173A HIS* 1.3 58.3 + - - +
175A LEU* 3.1 7.8 + - - +
176A LEU* 2.8 46.3 + - + +
193A ALA* 4.0 15.7 - - + +
194A ILE* 4.6 2.9 - - + +
197A SER* 2.9 26.0 + - - +
313A MET* 4.2 8.9 - - + +
314A VAL* 3.8 17.1 - - + +
317A ALA* 3.4 16.8 - - - +
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Residues in contact with HIS 173 (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 VAL* 3.3 24.2 + - - +
100A ASN* 2.8 29.5 + - - -
125A ILE* 3.6 37.3 - - + +
128A GLU* 4.3 10.9 - - + +
129A ARG* 2.9 68.3 + - + +
169A VAL 2.9 13.7 + - - +
170A GLN 3.4 8.3 - - - +
171A SER 3.2 0.2 - - - -
172A THR* 1.3 77.3 - - - +
174A VAL* 1.3 62.9 + - + +
176A LEU* 3.5 8.0 + - - -
177A SER* 3.3 8.9 + - - -
194A ILE* 5.0 3.5 - - + +
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Residues in contact with VAL 174 (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 VAL 3.9 3.1 - - - +
100A ASN* 3.6 31.0 - - - +
101A LYS 4.1 4.7 - - - +
102A TRP* 3.8 29.4 - - + +
170A GLN* 3.0 36.3 + - - +
171A SER 3.2 5.6 + - - +
173A HIS* 1.3 75.6 - - - +
175A LEU* 1.3 63.6 + - - +
177A SER* 3.0 20.9 + - - -
178A THR* 3.6 4.7 + - - -
516A EDO 4.3 13.2 + - - +
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Residues in contact with LEU 175 (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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102A TRP* 4.0 13.2 - - + -
171A SER 3.0 20.7 + - - +
172A THR* 3.1 4.7 + - - +
174A VAL* 1.3 76.2 - - - +
176A LEU* 1.3 59.9 + - - +
178A THR* 2.5 24.9 + - - -
181A LEU* 3.8 9.2 - - - +
313A MET* 3.6 43.5 - - + +
316A CYS* 4.2 3.6 - - + -
317A ALA* 4.2 11.7 - - + +
381A TRP* 3.9 32.3 - - + -
384A TRP* 4.1 9.4 - - + +
395A ILE* 4.3 1.1 - - + -
516A EDO 3.4 26.9 - - - +
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Residues in contact with LEU 176 (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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129A ARG* 3.5 19.2 + - - +
172A THR* 2.8 27.1 + - + +
173A HIS* 4.4 2.0 - - - -
174A VAL 3.2 0.4 - - - -
175A LEU* 1.3 77.1 - - - +
177A SER* 1.3 60.2 + - - +
178A THR 3.3 1.5 + - - +
181A LEU* 4.3 17.3 - - - +
182A GLU* 5.8 0.5 - - - -
185A PHE* 4.2 20.3 - - + -
190A ILE* 4.2 28.3 - - + +
193A ALA* 4.3 4.3 - - + -
194A ILE* 3.9 33.4 - - + -
310A LEU* 4.4 8.3 - - + -
313A MET* 3.7 25.6 - - + -
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A ASN* 6.0 2.1 - - - +
129A ARG* 3.0 21.1 + - - +
173A HIS* 3.3 9.9 + - - -
174A VAL* 3.0 14.6 + - - -
176A LEU* 1.3 75.8 - - - +
178A THR* 1.3 65.1 + - - +
179A PRO* 3.3 7.1 - - - +
182A GLU* 6.3 0.2 - - - -
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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
------------------------------------------------------------
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