Contacts of the helix formed by residues 120 - 126 (chain C) in PDB entry 3P1M
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 GLU 120 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.8 17.3 - - - +
188A LEU* 5.7 1.6 - - - +
119C PHE* 1.3 74.8 - - - +
121C ASP* 1.3 68.4 + - - +
122C HIS* 3.2 21.1 + - + +
123C ILE* 3.0 12.4 + - + +
124C TYR* 2.9 20.1 + - - +
162C ASN 4.9 0.2 - - - +
163C MET* 3.4 13.5 - - - +
164C THR* 2.7 49.1 + - - +
183F THR* 4.0 18.8 - - + +
191F GLN* 5.5 4.2 + - - -
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Residues in contact with ASP 121 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 3.8 4.7 - - + +
181A GLY 3.4 15.0 - - - +
182A LYS* 3.5 28.0 - - + -
183A THR* 4.5 4.0 + - - -
184A SER 5.4 3.1 - - - +
119C PHE 3.8 1.2 + - - -
120C GLU* 1.3 72.1 - - - +
122C HIS* 1.3 66.2 + - - +
124C TYR* 3.3 2.8 + - - +
125C GLU* 3.2 22.7 + - - +
147C ARG* 2.7 38.6 + - - +
121G ASP* 3.4 26.0 - - - +
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Residues in contact with HIS 122 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 4.0 21.8 - - + -
184A SER 4.3 10.4 + - - -
185A ALA* 4.4 7.2 - - + -
186A GLU* 3.3 57.9 + - + +
188A LEU* 5.7 2.0 - - - +
120C GLU* 4.0 27.1 + - + +
121C ASP* 1.3 82.1 + - - +
123C ILE* 1.3 87.4 + - + +
125C GLU* 3.7 10.1 + - - +
126C LYS* 3.8 5.0 + - - +
163C MET* 6.1 0.2 - - - +
189D TYR* 3.2 36.3 - + + -
190D PHE 5.1 0.4 - - - +
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Residues in contact with ILE 123 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C PHE* 4.4 9.6 - - + -
120C GLU* 3.0 18.7 + - + +
122C HIS* 1.3 91.8 - - + +
124C TYR* 1.3 66.2 + - - +
126C LYS* 3.4 10.2 + - - +
127C LEU* 3.3 28.3 + - + +
159C SER 4.5 6.7 - - - +
160C MET* 4.7 10.5 - - + -
163C MET* 4.1 40.6 - - + -
189D TYR* 3.4 36.7 + - + +
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Residues in contact with TYR 124 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180A VAL* 4.0 23.3 - - + -
119C PHE* 4.3 6.9 - - + +
120C GLU 2.9 11.3 + - - +
121C ASP 3.4 8.1 - - - +
123C ILE* 1.3 77.2 - - - +
125C GLU* 1.3 66.2 - - - +
127C LEU* 3.2 29.2 + - + +
145C THR 5.4 0.3 + - - -
146C ASP* 3.5 22.4 + - - -
147C ARG* 3.7 47.3 - - - -
148C SER 3.9 13.7 + - - -
149C ARG* 4.2 21.7 + - + -
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Residues in contact with GLU 125 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A ASP* 5.1 7.8 - - - +
180A VAL* 3.8 27.8 + - + +
182A LYS* 3.1 38.3 + - - +
121C ASP 3.2 12.5 + - - +
122C HIS 3.9 5.4 - - - +
123C ILE 3.3 0.2 - - - -
124C TYR* 1.3 86.9 - - - +
126C LYS* 1.3 77.8 + - + +
127C LEU 3.4 3.2 + - - +
190D PHE 4.6 0.2 - - - +
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Residues in contact with LYS 126 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182A LYS* 5.3 0.4 - - - +
122C HIS 3.8 2.4 + - - +
123C ILE 3.4 5.1 + - - -
124C TYR 3.2 0.8 - - - -
125C GLU* 1.3 98.7 + - + +
127C LEU* 1.3 65.7 + - - +
128C ASP* 3.9 2.1 + - - +
160C MET* 6.1 0.2 - - - +
187D ASN* 3.9 30.3 + - - +
188D LEU 3.3 25.9 + - - +
189D TYR* 3.8 31.9 - - + +
190D PHE* 4.0 27.1 + - - +
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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