Contacts of the helix formed by residues 192 - 202 (chain C) in PDB entry 1MA1
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 192 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85C GLY 4.0 9.9 + - - -
86C ASN* 3.0 27.5 + - - -
87C MET 3.9 15.2 + - - -
88C GLY* 5.1 0.6 - - - -
93C CYS* 4.0 18.7 - - - -
190C ILE 3.3 1.0 + - - -
191C VAL* 1.3 71.8 - - - +
193C TRP* 1.3 60.4 + - - +
194C LYS* 3.2 25.1 + - - +
195C GLU* 3.2 21.0 + - - +
196C VAL* 3.3 15.1 + - - +
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Residues in contact with TRP 193 (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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93C CYS* 5.5 0.6 - - - +
94C GLY 3.2 25.5 + - - +
95C GLY 3.0 20.1 + - - -
96C GLU* 3.6 10.7 - - - +
97C PRO* 3.5 23.8 - - + -
101C LEU* 3.9 20.6 - - + -
105C ILE* 4.8 2.2 - - + -
112C PHE* 3.7 20.0 - + - -
115C PHE* 3.8 26.0 - + - -
134C LEU* 5.5 1.3 - - + -
163C LEU* 4.0 23.1 - - + -
188C TRP* 3.8 17.4 - + - -
191C VAL* 3.4 22.1 + - + +
192C ASN* 1.3 70.3 + - - +
194C LYS* 1.3 62.8 + - + +
196C VAL* 3.9 13.9 - - + +
197C GLU* 2.8 49.2 + - - +
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Residues in contact with LYS 194 (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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92C GLU 5.5 6.3 - - - +
93C CYS* 6.4 0.2 - - - -
98C SER* 5.3 3.8 + - - -
192C ASN* 3.2 12.1 + - - +
193C TRP* 1.3 79.8 - - + +
195C GLU* 1.3 57.6 + - - +
197C GLU* 3.4 22.3 + - - +
198C LYS* 2.9 29.0 + - - +
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Residues in contact with GLU 195 (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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85C GLY* 3.2 29.2 - - - +
86C ASN* 4.4 1.1 - - - -
192C ASN* 3.2 18.6 + - - +
193C TRP 3.2 0.4 - - - -
194C LYS* 1.3 76.6 - - - +
196C VAL* 1.3 60.7 + - - +
198C LYS* 3.1 21.5 + - - +
199C ARG* 2.9 72.5 + - - +
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Residues in contact with VAL 196 (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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86C ASN* 3.8 18.8 - - + -
101C LEU* 3.7 20.9 - - + -
134C LEU* 5.0 1.8 - - + -
162C LEU* 3.4 42.1 - - + +
163C LEU* 4.0 19.7 - - + -
191C VAL* 4.8 1.1 - - + -
192C ASN 3.5 14.1 - - - +
193C TRP* 3.3 19.7 + - + +
195C GLU* 1.3 75.0 - - - +
197C GLU* 1.3 58.2 + - - +
199C ARG* 3.2 3.0 + - - +
200C PHE* 2.9 28.4 + - - +
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Residues in contact with GLU 197 (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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97C PRO* 3.3 11.3 - - - +
98C SER* 2.9 51.1 + - - +
101C LEU* 4.0 19.7 - - + +
193C TRP* 2.8 31.9 + - - +
194C LYS* 3.4 26.2 + - - +
196C VAL* 1.3 72.4 - - - +
198C LYS* 1.3 59.3 + - - +
200C PHE* 3.2 6.1 + - - +
201C GLU* 2.8 37.8 + - - +
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Residues in contact with LYS 198 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113B GLU* 6.4 2.0 - - + -
116B ARG* 5.4 7.9 - - - +
194C LYS 2.9 16.2 + - - +
195C GLU* 3.1 24.8 + - - +
197C GLU* 1.3 72.5 - - - +
199C ARG* 1.3 65.5 + - - +
201C GLU* 3.0 20.4 + - + +
202C ASP* 3.3 29.5 + - - +
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Residues in contact with ARG 199 (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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82C PHE* 2.8 55.7 + - + +
85C GLY* 3.5 9.7 - - - -
86C ASN* 3.0 33.7 + - - +
161C ILE 3.8 12.8 - - - +
162C LEU* 2.8 44.5 + - + +
163C LEU* 4.3 0.2 - - - +
195C GLU* 2.9 45.4 + - - +
196C VAL* 3.4 7.2 - - - +
198C LYS* 1.3 74.3 - - + +
200C PHE* 1.3 61.7 + - - +
202C ASP* 3.3 20.6 + - - +
203C ILE* 3.9 8.8 + - - +
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Residues in contact with PHE 200 (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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100C LYS* 3.9 9.6 - - + -
101C LEU* 3.7 39.9 - - + -
104C TYR* 3.4 50.0 - + + -
136C TYR* 4.0 18.6 - + - -
143C LEU* 3.9 17.0 - - + -
162C LEU* 3.5 27.8 - - + -
196C VAL 2.9 17.4 + - - +
197C GLU* 3.6 7.6 - - - +
198C LYS 3.1 0.4 - - - -
199C ARG* 1.3 76.9 - - - +
201C GLU* 1.3 65.2 + - + +
203C ILE* 3.4 16.2 + - + +
204C LEU 3.5 21.1 + - - +
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Residues in contact with GLU 201 (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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100C LYS* 4.8 28.2 + - + +
197C GLU* 2.8 31.5 - - - +
198C LYS* 3.0 10.4 + - + +
200C PHE* 1.3 84.5 - - + +
202C ASP* 1.3 61.5 + - - +
203C ILE 3.1 4.5 + - - -
204C LEU* 3.2 14.1 + - - +
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Residues in contact with ASP 202 (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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198C LYS* 3.3 33.5 - - - +
199C ARG* 3.3 10.6 + - - +
200C PHE 3.3 1.0 - - - -
201C GLU* 1.3 80.5 - - - +
203C ILE* 1.3 66.8 + - + +
204C LEU 3.6 0.2 - - - -
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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