Contacts of the helix formed by residues 197 - 208 (chain Q) in PDB entry 1H2I
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 197 (chain Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192Q LYS* 2.7 39.7 - - - +
195Q ASP 3.4 3.2 + - - +
196Q LEU* 1.3 77.4 - - - +
198Q PRO* 1.3 65.4 - - - +
199Q SER* 3.4 11.2 + - - -
200Q VAL* 3.3 20.5 + - + -
201Q GLU* 2.8 30.1 + - - +
42R ALA* 3.7 21.2 - - + +
45R GLN* 3.1 23.0 + - - +
77R GLU* 4.6 9.3 + - - +
78R MET* 3.9 18.2 - - + -
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Residues in contact with PRO 198 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194Q GLN* 5.9 3.4 - - - +
196Q LEU* 3.4 27.6 - - + +
197Q GLU* 1.3 84.1 - - - +
199Q SER* 1.3 67.6 + - - +
201Q GLU* 3.8 4.4 - - + +
202Q GLU* 3.1 31.7 + - + +
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Residues in contact with SER 199 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197Q GLU* 4.0 10.2 + - - -
198Q PRO* 1.3 80.5 - - - +
200Q VAL* 1.3 73.9 + - - +
202Q GLU* 3.4 11.5 - - - +
203Q ALA* 3.3 21.8 + - - +
34R GLU* 5.4 0.3 - - - +
38R ALA* 3.8 16.2 + - - +
42R ALA* 5.1 1.2 - - - +
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Residues in contact with VAL 200 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197Q GLU* 3.3 26.7 + - + +
198Q PRO 3.2 0.2 - - - -
199Q SER* 1.3 75.9 - - - +
201Q GLU* 1.3 65.6 + - - +
202Q GLU 2.9 2.1 + - - -
203Q ALA* 3.2 2.3 + - - +
204Q ARG* 2.9 59.5 + - - +
35R GLU* 5.1 1.7 - - + +
38R ALA* 3.8 20.6 - - + +
39R ILE* 3.9 12.3 - - + +
42R ALA* 3.9 22.4 - - + -
77R GLU 4.5 0.7 - - - +
78R MET* 3.4 13.5 - - - +
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Residues in contact with GLU 201 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196Q LEU* 4.4 12.6 - - + -
197Q GLU 2.8 20.9 + - - +
198Q PRO* 3.4 9.2 + - + +
200Q VAL* 1.3 72.7 - - - +
202Q GLU* 1.3 60.8 + - - +
204Q ARG* 3.3 23.9 + - - +
205Q TYR* 3.3 22.0 + - - +
77R GLU* 4.8 3.3 - - - +
36S TYR* 3.7 23.3 + - - -
37S GLN* 5.1 8.7 - - - +
40S GLN* 4.3 11.9 - - - +
41S LYS* 5.7 2.1 - - - +
44S ARG* 4.4 21.7 + - - +
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Residues in contact with GLU 202 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198Q PRO* 3.1 16.7 + - - +
199Q SER* 3.4 15.5 - - - +
200Q VAL 3.0 0.2 - - - -
201Q GLU* 1.3 72.9 - - - +
203Q ALA* 1.3 67.5 + - - +
204Q ARG 3.0 1.1 - - - -
205Q TYR* 3.0 14.9 + - - +
206Q ASN* 3.0 22.5 + - - +
34R GLU* 4.7 7.5 - - - +
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Residues in contact with ALA 203 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199Q SER 3.3 9.1 + - - +
200Q VAL 3.2 6.6 + - - +
202Q GLU* 1.3 79.6 - - - +
204Q ARG* 1.3 64.2 + - - +
206Q ASN* 3.0 13.5 + - - +
207Q SER* 3.4 9.9 + - - -
32R THR* 4.7 2.3 + - - -
34R GLU* 3.5 49.4 + - + +
35R GLU* 3.6 17.0 - - - +
38R ALA* 4.2 5.4 - - + -
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Residues in contact with ARG 204 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200Q VAL* 2.9 37.3 + - - +
201Q GLU* 3.3 23.6 + - - +
203Q ALA* 1.3 77.6 - - - +
205Q TYR* 1.3 60.0 + - - +
206Q ASN 2.7 6.9 + - - -
207Q SER* 2.8 24.3 + - - +
208Q CYS* 3.5 5.7 + - - +
35R GLU* 2.8 47.4 + - - +
39R ILE* 4.2 1.2 - - - +
77R GLU 3.0 27.3 + - - -
78R MET 3.2 17.5 + - - -
79R PHE* 3.7 18.8 - - - +
80R GLY* 3.9 5.3 - - - +
82R ASN* 5.4 0.9 - - - +
116R LYS* 4.3 9.4 - - - +
36S TYR* 2.8 39.9 + - + +
40S GLN* 4.5 0.8 + - - -
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Residues in contact with TYR 205 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201Q GLU* 3.3 11.1 + - - +
202Q GLU* 3.0 10.6 + - - +
204Q ARG* 1.3 77.7 - - - +
206Q ASN* 1.3 61.2 + - - +
207Q SER 3.5 0.2 - - - -
208Q CYS* 4.4 5.4 + - + +
209Q ARG* 3.3 47.4 + - - +
33S ALA* 2.9 50.2 + - + +
34S GLU* 3.5 13.0 + - - +
36S TYR* 4.3 15.0 - + + -
37S GLN* 3.1 42.6 + - + +
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Residues in contact with ASN 206 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202Q GLU* 3.0 20.0 + - - +
203Q ALA 3.4 6.5 - - - +
204Q ARG 2.7 1.6 + - - -
205Q TYR* 1.3 82.3 - - - +
207Q SER* 1.3 60.1 + - - +
209Q ARG* 3.0 49.2 + - - +
32R THR* 5.5 0.4 - - - -
34R GLU* 2.9 35.8 + - + +
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Residues in contact with SER 207 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203Q ALA 3.4 3.2 + - - -
204Q ARG* 2.8 20.4 + - - +
206Q ASN* 1.3 76.3 - - - +
208Q CYS* 1.3 58.1 + - - +
209Q ARG 2.7 21.0 + - - +
32R THR* 3.2 41.2 - - - +
35R GLU* 3.3 20.1 + - - -
116R LYS* 4.5 5.4 + - - -
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Residues in contact with CYS 208 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204Q ARG 3.5 6.8 + - - +
205Q TYR* 4.4 6.2 - - + +
207Q SER* 1.3 81.4 + - - +
209Q ARG* 1.3 56.7 + - - +
82R ASN* 5.7 2.9 - - - -
116R LYS* 6.1 2.7 - - - -
30S GLN* 5.0 10.8 - - - -
31S TYR* 3.6 25.4 - - - -
32S THR 4.5 0.4 - - - -
33S ALA* 3.5 40.5 + - + +
36S TYR* 4.6 15.5 - - + -
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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