Contacts of the helix formed by residues 158 - 170 (chain A) in PDB entry 3N1Q
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 LYS 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TRP* 3.5 62.7 - - + +
121A VAL* 4.8 4.3 - - + -
151A THR* 4.0 14.4 - - + +
153A ASP* 3.0 26.6 + - - +
155A ASP* 2.7 40.1 + - + +
156A ARG 2.8 1.4 + - - -
157A ASN* 1.3 83.4 - - + +
159A TYR* 1.3 55.2 + - - +
160A GLY 3.1 2.5 - - - -
161A LEU* 3.1 7.4 + - - +
162A LEU* 2.7 34.8 + - - +
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Residues in contact with TYR 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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150A THR* 3.5 18.3 - - - +
151A THR* 3.5 27.8 - - - -
154A ARG* 3.3 22.3 - - - +
155A ASP 3.5 12.6 - - - -
156A ARG* 2.9 55.6 + - + +
158A LYS* 1.3 79.1 - - - +
160A GLY* 1.3 63.0 + - - +
162A LEU* 3.5 14.7 - - + +
163A ALA* 3.0 24.3 + - - +
176A TYR* 3.4 20.8 - + + +
179A ARG 3.7 14.8 - - - -
180A ASN 3.7 15.3 - - - -
181A HIS* 4.4 3.6 - - - -
182A VAL* 3.7 15.1 - - + +
870D ASP* 5.1 0.5 + - - -
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Residues in contact with GLY 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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42A PRO* 3.5 5.3 - - - +
43A LEU 2.9 34.8 + - - -
156A ARG 4.2 2.0 + - - -
157A ASN 4.9 2.0 - - - -
158A LYS 3.1 1.0 - - - -
159A TYR* 1.3 80.2 - - - +
161A LEU* 1.3 59.8 + - - +
163A ALA* 3.5 8.8 + - - +
164A ARG 3.6 1.0 + - - -
176A TYR* 3.4 22.5 + - - -
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Residues in contact with LEU 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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40A LEU* 4.2 17.0 - - + +
42A PRO* 3.8 24.4 - - + +
117A MET* 3.5 42.0 - - + -
118A TRP* 3.5 19.7 - - + +
157A ASN 5.4 1.9 + - - +
158A LYS* 3.1 10.0 + - - +
160A GLY* 1.3 73.9 - - - +
162A LEU* 1.3 66.1 + - - +
164A ARG* 2.9 22.8 + - + -
165A LEU* 3.0 18.3 + - + +
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Residues in contact with LEU 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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110A LEU* 4.4 4.8 - - + +
114A VAL* 3.7 29.6 - - + -
118A TRP* 4.0 17.7 - - + -
123A LEU* 4.3 8.3 - - + -
149A ILE* 3.9 24.2 - - + +
150A THR* 3.7 37.0 - - - +
151A THR* 3.9 9.2 - - + +
158A LYS 2.7 21.2 + - - +
159A TYR* 3.5 13.0 - - + +
161A LEU* 1.3 74.0 - - - +
163A ALA* 1.3 61.1 + - - +
165A LEU* 3.2 7.8 + - + +
166A ALA* 3.1 21.1 + - - +
182A VAL* 4.7 3.1 - - + -
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Residues in contact with ALA 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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43A LEU* 3.8 21.1 - - + -
159A TYR 3.0 12.7 + - - +
160A GLY 3.6 11.0 - - - +
161A LEU 3.1 0.2 - - - -
162A LEU* 1.3 76.8 - - - +
164A ARG* 1.3 62.2 + - - +
166A ALA* 3.1 9.6 + - - -
167A VAL* 3.2 8.2 + - - +
174A VAL* 3.2 35.0 - - + +
176A TYR* 4.7 6.3 - - + -
182A VAL* 4.0 16.5 - - + +
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Residues in contact with ARG 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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39A GLN 4.2 7.4 - - - -
40A LEU* 3.7 24.9 - - + -
41A VAL* 2.7 50.7 + - - +
42A PRO* 4.1 9.8 + - + -
43A LEU* 3.5 26.9 - - - +
47A GLN* 5.7 0.6 - - - +
49A VAL* 4.6 9.7 - - - +
160A GLY 3.6 2.0 + - - -
161A LEU* 2.9 12.0 + - + +
163A ALA* 1.3 78.7 - - - +
165A LEU* 1.3 62.8 + - - +
167A VAL* 3.0 37.5 + - - +
168A GLU* 3.1 40.2 + - + +
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Residues in contact with LEU 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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40A LEU* 4.0 19.5 - - + -
110A LEU* 3.4 14.8 - - + +
113A ALA* 3.8 39.0 - - + +
114A VAL* 4.5 4.0 - - + +
117A MET* 3.9 37.7 - - + -
118A TRP* 4.4 15.7 - - + -
161A LEU* 3.0 16.7 + - + +
162A LEU* 3.2 8.7 + - - +
164A ARG* 1.3 76.4 - - - +
166A ALA* 1.3 57.1 + - - +
168A GLU* 3.4 8.8 + - + +
169A ALA* 2.8 29.1 + - - +
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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
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110A LEU* 3.8 16.2 - - + -
149A ILE* 4.8 1.1 - - + -
162A LEU 3.1 11.5 + - - +
163A ALA* 3.3 11.0 - - - +
164A ARG 3.1 0.4 - - - -
165A LEU* 1.3 75.1 - - - +
167A VAL* 1.3 63.5 + - - +
169A ALA* 3.3 6.6 + - - -
171A PHE* 3.1 31.4 + - + +
174A VAL* 3.5 20.4 - - + -
184A VAL* 3.7 20.4 - - + -
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Residues in contact with VAL 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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43A LEU* 4.8 2.5 - - + -
49A VAL* 4.0 32.1 - - + +
163A ALA 3.4 15.3 - - - +
164A ARG* 3.0 33.1 + - - +
166A ALA* 1.3 77.4 - - - +
168A GLU* 1.3 60.4 + - - +
170A GLY* 3.1 18.7 + - - -
171A PHE 4.0 8.3 + - - +
174A VAL* 3.6 22.2 - - + -
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Residues in contact with GLU 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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39A GLN 4.4 6.8 - - - +
40A LEU* 4.8 9.0 - - + -
164A ARG* 3.1 51.5 + - + +
165A LEU* 3.9 10.1 - - + +
167A VAL* 1.3 76.5 - - - +
169A ALA* 1.3 60.2 + - - +
170A GLY* 3.1 6.2 + - - -
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Residues in contact with ALA 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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105A GLU 5.0 0.3 - - - +
106A ARG* 3.5 21.7 - - - +
109A ALA* 4.0 16.7 - - - +
110A LEU* 3.8 31.9 - - + +
113A ALA* 5.8 1.6 - - + -
165A LEU 2.8 18.3 + - - +
166A ALA* 3.4 10.3 - - - +
167A VAL 3.2 0.2 - - - -
168A GLU* 1.3 76.6 - - - +
170A GLY* 1.3 58.5 + - - +
171A PHE* 3.6 4.0 - - + -
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Residues in contact with GLY 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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102A ARG* 4.8 0.3 + - - -
106A ARG* 2.7 31.0 + - - +
167A VAL 3.1 8.0 + - - -
168A GLU 3.1 5.7 - - - -
169A ALA* 1.3 77.7 - - - +
171A PHE* 1.3 65.0 + - - +
172A ASP* 3.5 9.5 + - - +
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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