Contacts of the helix formed by residues 163 - 177 (chain A) in PDB entry 3PIT
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 163 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A ILE* 3.7 24.8 - - + +
154A GLU* 2.8 27.6 + - - +
155A THR* 4.1 1.1 - - + -
161A PRO 4.2 0.8 + - - -
162A LEU* 1.3 90.0 - - - +
164A VAL* 1.3 56.3 + - - +
165A ASP 3.6 1.8 - - - -
166A LYS* 3.8 23.8 - - + +
167A THR* 2.7 37.2 + - - -
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Residues in contact with VAL 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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29A LEU* 3.5 44.0 - - + +
32A GLN* 4.0 10.8 - - + -
33A PHE* 3.7 23.8 - - + +
155A THR* 4.9 1.6 - - - -
156A SER 3.6 23.8 - - - +
161A PRO* 3.9 16.3 - - + -
162A LEU 3.7 4.9 - - - +
163A ASN* 1.3 75.2 - - - +
165A ASP* 1.3 69.3 + - - +
167A THR* 3.3 11.5 + - - -
168A PHE* 3.3 21.6 + - + -
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Residues in contact with ASP 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN 5.4 0.5 - - - +
33A PHE* 3.4 32.9 - - - +
36A LYS* 4.4 16.6 + - - -
163A ASN 3.6 0.2 - - - -
164A VAL* 1.3 78.5 - - - +
166A LYS* 1.3 57.7 + - - +
167A THR 3.3 0.2 + - - -
168A PHE* 3.4 0.5 + - - -
169A HIS* 2.9 52.4 + - + +
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Residues in contact with LYS 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153A ILE* 3.6 20.9 - - + -
163A ASN* 3.6 26.5 + - - +
164A VAL 3.3 0.4 - - - -
165A ASP* 1.3 78.7 - - - +
167A THR* 1.3 52.0 + - - +
169A HIS* 4.5 5.6 - - - -
170A ASP* 2.7 70.6 + - - +
173A ARG* 4.9 4.6 - - - +
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Residues in contact with THR 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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29A LEU* 6.3 1.1 - - + -
89A LEU* 3.6 30.2 - - + +
122A ILE* 3.9 4.9 - - + +
124A VAL* 3.7 22.7 - - + -
153A ILE* 3.4 20.1 - - + +
155A THR* 3.2 18.2 - - + +
163A ASN 2.7 25.9 + - - -
164A VAL* 3.7 5.2 - - - -
165A ASP 3.2 0.2 - - - -
166A LYS* 1.3 76.8 - - - +
168A PHE* 1.3 64.2 + - + +
170A ASP* 3.8 3.7 - - - +
171A LEU* 3.2 21.8 + - - +
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Residues in contact with PHE 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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16A LEU* 4.2 21.5 - - + +
18A VAL* 4.0 6.1 - - + -
29A LEU* 3.9 16.4 - - + -
30A THR* 4.0 24.7 - - - -
33A PHE* 3.5 56.8 - + + -
56A ILE* 5.9 0.2 - - - -
63A LEU* 5.4 0.4 - - + -
65A VAL* 3.9 24.7 - - + -
89A LEU* 3.7 28.7 - - + -
164A VAL* 3.3 25.4 + - + -
165A ASP 4.1 0.2 - - - +
167A THR* 1.3 80.3 - - - +
169A HIS* 1.3 64.6 + - - +
171A LEU* 3.3 8.1 + - - +
172A VAL* 3.2 24.4 + - - +
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Residues in contact with HIS 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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33A PHE* 3.8 29.3 - + - -
52A LYS* 6.3 0.2 - - - -
54A THR* 5.3 4.7 - - - -
55A GLU 5.8 0.6 + - - -
56A ILE* 3.7 35.6 - - + +
63A LEU* 5.4 0.2 - - + -
165A ASP* 2.9 33.6 + - + +
166A LYS* 4.0 1.6 - - - +
168A PHE* 1.3 76.8 - - - +
170A ASP* 1.3 59.0 + - - +
172A VAL* 3.1 9.5 + - - +
173A ARG* 2.9 60.9 + - - +
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Residues in contact with ASP 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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122A ILE* 3.6 18.4 - - + -
151A PRO* 6.2 0.6 - - + +
153A ILE* 4.4 4.8 - - + +
166A LYS* 2.7 59.0 + - - +
167A THR* 3.8 1.6 - - - +
169A HIS* 1.3 73.7 - - - +
171A LEU* 1.3 56.7 - - - +
173A ARG* 2.9 33.4 + - - +
174A VAL* 2.9 32.7 + - + +
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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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16A LEU* 3.8 28.0 - - + -
87A GLY* 3.6 28.7 - - - +
88A PHE 3.6 26.2 - - - +
89A LEU* 3.7 26.9 - - + +
120A PRO* 4.1 4.3 - - + -
121A MET* 4.0 15.9 - - - +
122A ILE* 3.4 12.0 - - + +
167A THR 3.2 13.3 + - - +
168A PHE* 3.6 9.4 - - - +
170A ASP* 1.3 75.8 - - - +
172A VAL* 1.3 62.9 + - - +
174A VAL* 3.2 4.5 + - + +
175A ILE* 3.0 28.2 + - - +
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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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14A TYR* 3.8 18.4 - - + -
16A LEU* 3.9 14.6 - - + -
56A ILE* 4.2 16.4 - - + -
63A LEU* 3.7 26.9 - - + -
168A PHE 3.2 12.3 + - - +
169A HIS 3.1 9.5 + - - +
171A LEU* 1.3 76.7 - - - +
173A ARG* 1.3 56.6 + - - +
175A ILE* 3.2 9.0 + - - +
176A ARG* 2.9 63.9 + - - +
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Residues in contact with ARG 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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56A ILE* 4.2 7.3 - - + +
57A ASP* 2.7 43.4 + - - +
166A LYS* 4.4 7.7 + - - +
169A HIS* 2.9 46.9 + - - +
170A ASP* 2.9 35.9 + - - +
172A VAL* 1.3 75.7 - - + +
174A VAL* 1.3 57.3 + - + +
176A ARG* 3.2 8.7 + - - +
177A GLN* 2.9 55.4 + - - +
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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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120A PRO* 3.7 30.3 - - + -
121A MET 4.5 4.7 - - - +
122A ILE* 4.5 7.4 - - + -
151A PRO* 4.3 24.9 - - + -
170A ASP* 2.9 20.5 + - + +
171A LEU* 3.2 10.3 + - + +
173A ARG* 1.3 75.7 - - + +
175A ILE* 1.3 64.6 + - - +
177A GLN* 3.3 14.7 + - - +
178A GLN* 3.5 14.7 + - + +
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Residues in contact with ILE 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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14A TYR* 3.8 28.5 - - + -
16A LEU* 3.5 31.6 - - + -
86A ASP* 3.4 40.4 - - + +
87A GLY* 3.9 2.9 - - - +
120A PRO* 3.8 11.7 - - + -
171A LEU* 3.0 19.2 + - + +
172A VAL* 3.6 8.7 - - - +
174A VAL* 1.3 76.3 - - - +
176A ARG* 1.3 61.7 + - - +
177A GLN 3.5 0.2 + - - -
178A GLN* 3.4 29.4 - - - +
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Residues in contact with ARG 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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12A PRO* 5.5 0.2 - - - +
14A TYR* 2.9 29.6 + - + +
56A ILE* 2.9 36.0 + - - +
57A ASP* 4.1 5.3 + - - +
59A GLN* 3.0 59.0 + - - +
60A TRP 4.3 1.8 + - - -
61A ALA* 3.7 22.0 - - - +
172A VAL* 2.9 33.2 + - - +
173A ARG* 3.2 8.6 + - - +
175A ILE* 1.3 72.8 - - - +
177A GLN* 1.3 60.8 + - + +
178A GLN* 3.1 12.5 + - - +
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Residues in contact with GLN 177 (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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173A ARG* 2.9 37.6 + - - +
174A VAL* 3.3 8.6 + - - +
175A ILE 3.3 0.6 - - - -
176A ARG* 1.3 79.9 - - + +
178A GLN* 1.3 65.6 + - - +
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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