Contacts of the helix formed by residues 162 - 173 (chain A) in PDB entry 3N1O
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 162 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A TRP* 3.3 56.8 - - + +
125A VAL* 4.2 8.0 - - + +
155A THR* 4.0 21.1 - - + +
157A ASP* 2.6 31.4 + - - +
159A ASP* 2.7 44.4 + - - +
161A ASN* 1.3 71.6 - - + +
163A TYR* 1.3 57.6 + - - +
164A GLY 3.2 2.7 - - - -
165A LEU* 3.0 10.4 + - - +
166A LEU* 2.9 26.0 + - - +
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Residues in contact with TYR 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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153A ILE 5.3 0.2 - - - -
154A THR* 3.2 28.5 - - + +
155A THR* 3.6 20.4 - - - -
158A ARG* 3.4 22.2 + - - +
159A ASP 3.5 20.6 - - - -
160A ARG* 3.2 17.1 + - + +
162A LYS* 1.3 79.1 - - + +
164A GLY* 1.3 57.5 + - - +
166A LEU* 3.5 10.7 - - + +
167A ALA* 2.9 30.7 + - - +
180A TYR* 3.5 22.7 - - + +
182A SER 4.8 0.9 - - - -
183A LYS 3.4 21.3 - - - -
184A ALA* 3.3 32.4 + - - -
185A HIS* 3.9 8.3 - - - -
186A VAL* 3.7 10.7 - - + +
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Residues in contact with GLY 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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46A PRO* 3.4 10.7 - - - +
47A LEU 2.9 38.7 + - - -
161A ASN 4.5 4.0 + - - -
162A LYS 3.2 0.8 - - - -
163A TYR* 1.3 78.3 - - - +
165A LEU* 1.3 61.4 + - - +
167A ALA* 3.4 1.9 + - - +
168A ARG 3.3 10.6 + - - -
180A TYR* 3.5 16.2 + - - -
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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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44A LEU* 4.1 37.5 - - + +
46A PRO* 3.6 15.1 - - + +
121A GLN* 3.3 34.1 - - + +
122A TRP* 3.4 27.1 - - + +
161A ASN 5.2 1.4 + - - +
162A LYS* 3.0 11.0 + - - +
164A GLY* 1.3 72.8 - - - +
166A LEU* 1.3 66.8 + - - +
168A ARG* 3.0 8.3 + - + +
169A LEU* 3.0 23.4 + - + +
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Residues in contact with LEU 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A LEU* 4.7 2.0 - - + -
118A VAL* 3.7 30.5 - - + -
122A TRP* 3.9 11.5 - - + -
127A LEU* 4.1 13.5 - - + -
153A ILE* 3.8 23.8 - - + +
154A THR* 3.5 34.8 - - - +
155A THR* 3.8 15.9 - - + +
162A LYS 2.9 12.8 + - - +
163A TYR* 3.5 13.2 - - + +
165A LEU* 1.3 75.8 - - - +
167A ALA* 1.3 63.3 + - - +
169A LEU* 3.1 6.8 + - - +
170A ALA* 2.9 22.2 + - - +
186A VAL* 4.5 9.0 - - + -
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Residues in contact with ALA 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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47A LEU* 3.2 29.2 - - + -
163A TYR 2.9 16.7 + - - +
164A GLY* 3.6 5.6 - - - +
165A LEU 3.2 0.2 - - - -
166A LEU* 1.3 74.9 - - - +
168A ARG* 1.3 62.8 + - - +
170A ALA* 3.2 7.7 + - - +
171A VAL* 3.1 18.0 + - - +
178A VAL* 3.3 12.5 - - + +
180A TYR* 4.9 5.2 - - + -
186A VAL* 3.7 27.1 - - + +
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Residues in contact with ARG 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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44A LEU* 4.1 31.6 - - + +
45A VAL* 2.8 39.4 + - - +
46A PRO* 4.2 4.7 + - + -
47A LEU* 3.8 21.4 - - - +
51A GLN* 4.9 9.7 - - - +
53A SER* 4.9 7.2 + - - -
164A GLY 3.3 8.2 + - - +
165A LEU* 3.0 12.6 + - + +
167A ALA* 1.3 76.4 - - - +
169A LEU* 1.3 67.3 + - - +
171A VAL* 3.0 27.6 + - - +
172A GLU* 2.9 34.0 + - - +
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Residues in contact with LEU 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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44A LEU* 3.6 28.5 - - + -
114A LEU* 3.6 13.5 - - + +
117A SER* 4.1 25.8 + - - +
118A VAL* 4.4 7.9 - - + -
120A ASN* 6.3 0.9 - - - +
121A GLN* 3.9 23.3 - - + +
122A TRP* 3.9 33.4 - - + -
165A LEU* 3.0 17.1 + - + +
166A LEU* 3.1 7.8 + - - +
168A ARG* 1.3 75.2 - - - +
170A ALA* 1.3 52.5 + - - +
172A GLU* 3.0 11.6 + - + +
173A ALA* 2.7 35.2 + - - +
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Residues in contact with ALA 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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114A LEU* 3.4 21.9 - - + +
153A ILE* 4.4 1.3 - - + -
166A LEU 2.9 12.1 + - - +
167A ALA* 3.2 12.1 - - - +
169A LEU* 1.3 76.9 - - - +
171A VAL* 1.3 62.7 + - - +
173A ALA* 3.1 12.6 + - - +
174A GLY 3.3 0.2 + - - -
175A PHE* 3.3 22.4 + - + -
178A VAL* 3.8 16.4 - - + -
188A CYS* 3.8 19.7 - - - -
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Residues in contact with VAL 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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47A LEU* 4.1 10.8 - - + -
53A SER* 4.2 22.7 - - - +
167A ALA 3.1 13.9 + - - +
168A ARG* 3.0 30.7 + - - +
170A ALA* 1.3 76.6 - - - +
172A GLU* 1.3 61.7 + - - +
174A GLY* 2.9 21.8 + - - -
175A PHE 4.2 8.3 + - - +
178A VAL* 3.5 26.5 - - + -
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Residues in contact with GLU 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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44A LEU* 4.0 33.5 - - + +
168A ARG* 2.9 32.6 + - - +
169A LEU* 3.0 15.2 + - + +
171A VAL* 1.3 80.9 - - - +
173A ALA* 1.3 60.5 + - - +
174A GLY* 3.1 1.8 + - - -
83B PRO* 5.3 6.1 - - - +
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Residues in contact with ALA 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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110A ARG* 3.3 27.1 - - - +
113A SER* 4.6 4.7 - - - -
114A LEU* 3.9 24.0 - - + +
117A SER* 5.3 1.3 - - - +
169A LEU 2.7 16.4 + - - +
170A ALA* 3.4 11.0 - - - +
171A VAL 3.1 0.8 - - - -
172A GLU* 1.3 70.7 - - - +
174A GLY* 1.3 57.0 + - - +
175A PHE* 3.5 3.4 - - + -
83B PRO* 5.4 3.6 - - - -
85B TYR* 2.8 29.8 + - - -
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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