Contacts of the helix formed by residues 192 - 202 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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85D GLY 4.0 10.1 + - - -
86D ASN* 2.9 28.6 + - - -
87D MET 3.8 14.9 + - - -
88D GLY* 5.1 0.6 - - - -
93D CYS* 4.1 18.2 - - - -
190D ILE 3.3 1.2 + - - -
191D VAL* 1.3 69.9 - - - +
193D TRP* 1.3 62.6 + - - +
194D LYS* 3.1 24.0 + - - +
195D GLU* 3.2 22.5 + - - +
196D VAL* 3.3 15.4 + - - +
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Residues in contact with TRP 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D CYS* 5.7 0.8 - - - +
94D GLY 3.2 25.5 + - - +
95D GLY 3.0 20.3 + - - -
96D GLU* 3.6 10.2 - - - +
97D PRO* 3.5 25.8 - - + -
101D LEU* 3.8 20.0 - - + -
105D ILE* 4.8 2.5 - - + -
112D PHE* 3.7 19.5 - + - -
115D PHE* 3.8 25.8 - + - -
134D LEU* 5.5 1.3 - - + -
163D LEU* 3.9 22.7 - - + -
188D TRP* 3.8 17.2 + + - -
191D VAL* 3.4 20.2 + - + +
192D ASN* 1.3 71.0 + - - +
194D LYS* 1.3 58.0 + - + +
196D VAL* 3.8 14.1 - - + +
197D GLU* 2.7 53.3 + - - +
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Residues in contact with LYS 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92D GLU 5.6 6.3 - - - +
98D SER* 5.4 3.2 + - - -
192D ASN* 3.1 11.6 + - - +
193D TRP* 1.3 80.6 - - + +
195D GLU* 1.3 57.1 + - - +
197D GLU* 3.4 22.6 + - - +
198D LYS* 2.9 28.6 + - - +
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Residues in contact with GLU 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85D GLY* 3.3 28.7 - - - +
86D ASN* 4.5 1.1 - - - -
192D ASN* 3.2 19.2 + - - +
193D TRP 3.2 0.2 - - - -
194D LYS* 1.3 77.5 - - - +
196D VAL* 1.3 60.4 + - - +
198D LYS* 3.1 21.4 + - - +
199D ARG* 2.9 72.5 + - - +
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Residues in contact with VAL 196 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86D ASN* 3.8 17.9 - - + -
101D LEU* 3.6 22.2 - - + -
134D LEU* 5.0 1.6 - - + -
162D LEU* 3.5 40.1 - - + +
163D LEU* 3.9 20.0 - - + -
191D VAL* 4.7 1.1 - - + -
192D ASN 3.4 15.5 - - - +
193D TRP* 3.3 20.1 + - + +
195D GLU* 1.3 72.9 - - - +
197D GLU* 1.3 66.8 + - - +
199D ARG* 3.3 4.2 + - - +
200D PHE* 2.9 22.5 + - - +
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Residues in contact with GLU 197 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D PRO* 3.4 9.0 - - - +
98D SER* 3.0 47.9 + - - +
101D LEU* 4.0 22.2 - - + +
193D TRP* 2.7 29.4 + - - +
194D LYS* 3.4 27.2 + - - +
196D VAL* 1.3 72.9 - - - +
198D LYS* 1.3 60.3 + - - +
200D PHE* 3.2 6.1 + - - +
201D GLU* 2.8 37.6 + - - +
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Residues in contact with LYS 198 (chain D).
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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194D LYS 2.9 14.6 + - - +
195D GLU* 3.1 25.2 + - - +
197D GLU* 1.3 74.6 - - - +
199D ARG* 1.3 64.8 + - + +
201D GLU* 3.0 18.8 + - - +
202D ASP* 3.2 30.6 + - - +
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Residues in contact with ARG 199 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81D LEU 4.8 0.2 + - - -
82D PHE* 2.8 55.8 + - + +
85D GLY* 3.6 9.1 - - - -
86D ASN* 2.9 36.0 + - - +
161D ILE* 3.9 12.3 - - - +
162D LEU* 2.9 42.4 + - + +
163D LEU* 4.3 0.4 - - - +
195D GLU* 2.9 46.9 + - - +
196D VAL* 3.5 6.1 - - - +
198D LYS* 1.3 73.3 - - + +
200D PHE* 1.3 62.2 + - - +
202D ASP* 3.4 20.8 + - - +
203D ILE* 3.9 9.0 + - - +
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Residues in contact with PHE 200 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 3.9 10.5 - - + -
101D LEU* 3.7 41.7 - - + -
104D TYR* 3.5 49.6 - + + -
136D TYR* 4.0 18.4 - + - -
143D LEU* 3.9 16.2 - - + -
162D LEU* 3.4 27.6 - - + +
196D VAL 2.9 16.5 + - - +
197D GLU* 3.6 7.0 - - - +
198D LYS 3.1 0.4 - - - -
199D ARG* 1.3 77.6 - - - +
201D GLU* 1.3 65.3 + - + +
203D ILE* 3.4 16.5 + - + +
204D LEU 3.5 20.7 + - - +
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Residues in contact with GLU 201 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LYS* 4.7 26.9 + - + +
197D GLU* 2.8 32.1 - - - +
198D LYS* 3.0 9.3 + - - +
200D PHE* 1.3 78.7 - - + +
202D ASP* 1.3 61.7 + - - +
203D ILE 3.1 10.2 + - - -
204D LEU* 3.2 14.7 + - - +
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Residues in contact with ASP 202 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198D LYS* 3.2 35.6 + - - +
199D ARG* 3.9 9.1 - - - +
200D PHE 3.3 1.4 - - - -
201D GLU* 1.3 80.1 - - - +
203D ILE* 1.3 67.0 + - + +
204D 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