Contacts of the helix formed by residues 156 - 170 (chain I) in PDB entry 4P5O
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 156 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152I VAL* 2.7 31.2 + - + +
153I LEU 4.3 0.7 - - - -
154I GLN 3.6 0.2 - - - -
155I ASN* 1.3 77.6 - - + +
157I ARG* 1.3 58.2 + - - +
158I ARG* 3.0 25.1 + - - +
159I LEU* 2.8 46.1 + - + +
160I PHE* 2.9 19.6 + - - +
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Residues in contact with ARG 157 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I PHE* 3.2 41.3 - - + -
138I GLU* 5.9 1.0 + - - -
139I PRO* 5.2 9.1 + - - +
141I PRO* 6.1 1.6 - - - +
153I LEU* 4.0 32.9 + - + +
154I GLN 5.5 1.1 - - - +
155I ASN 4.2 0.8 + - - -
156I ASN* 1.3 71.6 + - - +
158I ARG* 1.3 67.4 + - - +
160I PHE* 3.3 6.2 + - - +
161I GLU* 2.9 25.5 + - - +
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Residues in contact with ARG 158 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156I ASN* 3.0 17.3 + - - +
157I ARG* 1.3 78.3 - - - +
159I LEU* 1.3 83.1 + - - +
161I GLU* 3.1 12.7 + - - +
162I GLN* 2.9 54.0 + - - +
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Residues in contact with LEU 159 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I VAL* 3.8 22.9 - - + -
156I ASN* 2.8 31.0 + - + +
158I ARG* 1.3 95.9 - - - +
160I PHE* 1.3 60.9 + - - +
162I GLN* 3.8 19.0 - - - +
163I ASN* 2.9 40.9 + - - +
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Residues in contact with PHE 160 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I PHE* 4.1 20.0 - + - -
71I TYR* 3.6 22.2 - + - -
100I TYR* 3.4 31.4 - + - -
102I PRO* 4.3 12.8 - - + -
139I PRO* 4.6 8.7 - - + -
149I ALA* 3.7 17.0 - - + -
152I VAL* 3.6 7.8 - - + +
153I LEU* 3.6 48.5 - - + -
156I ASN 2.9 20.7 + - - +
157I ARG* 3.7 5.8 - - - +
158I ARG 3.3 0.2 - - - -
159I LEU* 1.3 76.9 - - - +
161I GLU* 1.3 59.1 - - - +
163I ASN* 3.5 3.0 - - - +
164I VAL* 2.9 39.8 + - + +
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Residues in contact with GLU 161 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69I GLY 5.5 0.7 - - - +
70I PHE* 3.8 39.7 - - + +
157I ARG 2.9 16.9 + - - +
158I ARG* 3.4 9.4 - - - +
160I PHE* 1.3 76.2 - - - +
162I GLN* 1.3 66.7 + - - +
164I VAL* 3.2 4.5 + - - +
165I GLN* 2.9 29.7 + - + +
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Residues in contact with GLN 162 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158I ARG* 2.9 39.3 + - - +
159I LEU* 3.8 16.8 - - + +
161I GLU* 1.3 77.6 - - - +
163I ASN* 1.3 62.9 + - - +
165I GLN* 3.3 6.6 + - - +
166I ARG* 2.9 38.5 + - + +
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Residues in contact with ASN 163 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100I TYR* 2.9 41.0 + - + -
152I VAL* 4.4 11.5 - - - +
159I LEU* 2.9 32.4 + - - +
160I PHE 3.5 5.6 - - - +
162I GLN* 1.3 78.9 + - - +
164I VAL* 1.3 60.4 + - - +
166I ARG* 3.3 7.0 + - - +
167I SER* 2.8 29.5 + - - -
173I ILE* 4.0 29.0 - - + +
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Residues in contact with VAL 164 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I PHE* 3.4 28.9 - - + +
71I TYR* 3.4 42.0 - - + +
100I TYR* 3.6 17.7 - - + +
160I PHE* 2.9 40.7 + - + +
161I GLU* 3.7 5.8 - - - +
163I ASN* 1.3 72.9 - - - +
165I GLN* 1.3 63.9 + - - +
167I SER* 2.9 23.7 + - - +
168I MET* 3.0 14.9 + - + +
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Residues in contact with GLN 165 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70I PHE 5.3 4.7 - - - +
72I LYS 5.8 0.6 + - - -
73I SER* 5.3 6.9 + - - -
161I GLU* 2.9 17.3 + - + +
162I GLN* 3.4 12.1 - - - +
164I VAL* 1.3 77.0 - - - +
166I ARG* 1.3 59.3 + - - +
168I MET* 2.8 34.0 + - + +
169I ARG* 2.4 67.4 + - - +
182I LEU* 5.9 3.2 - - - +
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Residues in contact with ARG 166 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162I GLN* 2.9 26.6 + - + +
163I ASN* 3.8 7.4 - - - +
165I GLN* 1.3 76.2 - - - +
167I SER* 1.3 61.0 + - - +
169I ARG* 4.6 4.7 - - - +
170I GLY 3.3 30.0 + - - +
171I GLY* 3.9 6.7 + - - +
172I TYR 3.7 27.7 + - - +
173I ILE* 5.0 7.9 - - + +
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Residues in contact with SER 167 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I TYR* 5.5 0.3 - - - -
98I MET 5.2 0.9 - - - +
99I VAL* 5.1 3.1 - - - +
100I TYR* 3.6 34.2 + - - +
163I ASN 2.8 17.0 + - - -
164I VAL* 2.9 13.5 + - - +
165I GLN 3.1 0.2 - - - -
166I ARG* 1.3 78.8 - - - +
168I MET* 1.3 64.0 + - - +
170I GLY 3.8 2.6 + - - -
173I ILE* 4.0 11.0 - - - -
178I PHE* 3.6 30.8 - - - +
179I GLU 3.7 12.3 - - - +
181I CYS* 4.4 2.5 - - - -
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Residues in contact with MET 168 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70I PHE 3.8 11.2 - - - +
71I TYR* 3.7 20.9 - - + +
72I LYS 4.2 9.6 - - - +
73I SER* 4.7 2.7 - - - +
74I GLY* 4.2 9.4 - - - -
76I PHE* 3.6 24.7 - - + -
99I VAL* 5.7 0.9 - - + -
164I VAL* 3.0 32.2 + - + +
165I GLN* 2.8 20.4 + - + +
167I SER* 1.3 80.2 + - - +
169I ARG* 1.3 56.9 + - + +
170I GLY 3.2 4.9 - - - -
180I ARG* 3.3 5.9 - - - +
181I CYS* 3.1 45.3 + - - -
182I LEU* 3.5 17.5 - - + +
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Residues in contact with ARG 169 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165I GLN* 2.4 61.3 + - - +
166I ARG* 4.4 4.3 - - - +
168I MET* 1.3 79.2 - - + +
170I GLY* 1.3 64.3 + - - +
180I ARG* 2.3 47.1 + - - +
182I LEU* 4.3 16.6 - - + -
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Residues in contact with GLY 170 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166I ARG* 3.3 15.6 + - - +
167I SER 3.8 0.8 + - - -
168I MET 3.2 4.2 - - - -
169I ARG* 1.3 85.8 - - - +
171I GLY* 1.3 57.3 + - - -
177I TYR* 3.8 11.0 - - - -
178I PHE 3.1 14.1 - - - -
179I GLU 4.1 0.4 - - - -
180I ARG* 3.6 14.6 - - - -
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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