Contacts of the helix formed by residues 199 - 207 (chain D) in PDB entry 1IBM
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 199 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60D GLU* 2.5 25.3 + - - +
198D VAL* 1.3 72.8 - - - +
200D GLU* 1.3 74.0 + - - +
201D GLN* 3.0 32.8 - - - +
202D LEU* 2.9 40.0 + - + +
203D VAL 3.5 1.7 + - - -
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Residues in contact with GLU 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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90D GLY* 4.6 25.4 - - - +
91D SER 5.5 0.3 + - - -
93D PHE* 6.0 3.6 - - + -
94D LEU* 3.8 16.0 - - + +
191D ARG* 2.9 41.2 + - - +
198D VAL* 3.1 27.4 - - + +
199D ASN* 1.3 78.8 + - - +
201D GLN* 1.4 55.7 + - + +
203D VAL* 2.4 38.9 + - + +
204D ILE* 2.7 23.4 + - + +
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Residues in contact with GLN 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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199D ASN* 3.0 26.1 - - - +
200D GLU* 1.4 80.8 - - + +
202D LEU* 1.3 63.4 + - + +
204D ILE* 3.4 19.9 + - - +
205D GLU* 3.1 43.4 + - - +
97E GLY* 5.0 6.1 - - - +
99E GLY* 4.2 18.1 - - - +
100E VAL* 4.6 2.8 - - - +
116E THR* 3.6 29.4 + - - +
117E ASP* 4.9 3.0 + - - -
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Residues in contact with LEU 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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56D VAL* 3.6 24.2 - - + -
57D ARG* 4.1 27.2 - - - +
60D GLU* 3.8 33.0 - - + +
199D ASN* 2.9 28.4 + - + +
200D GLU 2.8 0.6 + - - -
201D GLN* 1.3 76.7 - - + +
203D VAL* 1.3 57.7 + - - +
205D GLU* 2.6 44.6 + - - +
206D PHE* 2.7 14.3 + - - +
111E GLU* 5.5 3.1 - - - +
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Residues in contact with VAL 203 (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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60D GLU* 4.2 8.2 - - + +
61D LYS* 3.5 38.6 - - + +
64D LEU* 4.6 15.0 - - + -
79D PHE* 4.5 9.0 - - + -
93D PHE* 4.2 29.2 - - + -
198D VAL* 4.9 0.4 - - + -
199D ASN 3.5 0.4 + - - -
200D GLU* 2.4 31.7 + - + +
202D LEU* 1.3 76.0 - - - +
204D ILE* 1.3 65.5 + - + +
206D PHE* 3.3 15.6 + - - +
207D TYR* 3.4 21.5 + - + -
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Residues in contact with ILE 204 (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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79D PHE* 4.1 28.5 - - + -
88D VAL* 5.5 0.7 - - + -
89D THR* 4.4 3.8 - - + -
90D GLY* 3.8 31.4 - - - +
200D GLU* 2.7 22.2 + - + +
201D GLN* 3.6 23.6 - - - +
203D VAL* 1.3 73.7 - - + +
205D GLU* 1.3 65.2 + - + +
207D TYR* 3.2 13.5 + - - +
208D SER* 3.1 17.0 + - - +
97E GLY* 3.6 31.6 - - - +
98E THR 4.0 13.5 - - - +
99E GLY* 5.2 1.3 - - - +
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Residues in contact with GLU 205 (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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8A A 2.6 31.5 + - - +
57D ARG* 2.4 45.7 + - - +
201D GLN* 3.1 23.0 + - - +
202D LEU* 2.6 21.1 + - - +
204D ILE* 1.3 76.9 - - - +
206D PHE* 1.3 49.9 + - - -
208D SER* 3.1 19.9 + - - -
98E THR 6.0 0.2 - - - -
99E GLY* 4.7 5.8 - - - -
100E VAL* 3.4 51.3 + - - +
101E ILE* 6.2 1.1 - - + -
107E ARG* 4.5 2.2 - - - +
111E GLU* 3.9 6.4 - - - +
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Residues in contact with PHE 206 (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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8A A 4.4 1.8 - - - +
545A C 5.8 0.9 - - - -
54D TYR* 3.7 25.6 - + - -
57D ARG* 3.7 39.6 - - + +
58D LEU* 3.4 38.8 - - + -
61D LYS* 3.8 20.9 - - + -
72D GLU* 5.2 1.1 - - - -
202D LEU 2.7 11.7 + - - +
203D VAL* 3.6 10.1 - - - +
204D ILE 3.1 0.2 - - - -
205D GLU* 1.3 70.5 - - - +
207D TYR* 1.3 97.7 + + - +
208D SER 3.0 5.5 + - - -
209D ARG* 3.6 18.7 + - - +
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Residues in contact with TYR 207 (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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61D LYS* 2.9 30.4 - - + +
72D GLU* 3.3 18.1 + - - -
75D PHE* 3.4 30.6 - + - -
76D ARG* 3.3 42.4 + - - +
79D PHE* 3.5 51.9 - + + -
80D GLU* 5.5 1.5 - - - +
203D VAL* 3.4 15.0 + - + -
204D ILE 3.2 6.1 + - - +
206D PHE* 1.3 97.1 - + - +
208D SER* 1.3 57.1 + - - +
209D ARG* 3.0 14.1 + - - +
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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