Contacts of the helix formed by residues 197 - 205 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192H LYS* 2.9 44.4 - - - +
195H ASP 3.2 4.2 + - - +
196H LEU* 1.3 76.6 - - - +
198H PRO* 1.4 55.9 - - - +
199H SER* 2.8 31.1 + - - +
200H VAL* 3.0 17.7 + - + +
201H GLU* 3.1 13.1 + - - +
42I ALA* 3.2 29.9 - - - +
45I GLN* 3.1 20.5 + - - +
77I GLU* 4.9 15.0 + - + +
78I MET* 3.8 8.5 - - + +
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Residues in contact with PRO 198 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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194H GLN* 5.9 0.7 - - - +
196H LEU* 3.3 27.9 - - + +
197H GLU* 1.4 82.0 - - - +
199H SER* 1.3 64.3 - - - +
201H GLU* 3.9 10.1 - - + -
202H GLU* 2.8 27.5 + - - +
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Residues in contact with SER 199 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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197H GLU* 3.3 24.6 + - - -
198H PRO* 1.3 81.3 - - - +
200H VAL* 1.3 68.7 + - - +
202H GLU* 3.2 13.2 + - - +
203H ALA* 3.3 12.5 + - - +
38I ALA* 4.4 9.7 + - - +
42I ALA* 5.2 0.5 - - - +
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Residues in contact with VAL 200 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197H GLU* 3.0 10.9 + - + +
199H SER* 1.3 81.7 + - - +
201H GLU* 1.3 68.9 + - - +
203H ALA* 3.0 4.5 + - - +
204H ARG* 2.9 37.5 + - - +
35I GLU* 4.7 3.8 - - + +
38I ALA* 3.6 39.7 - - + +
39I ILE* 3.5 25.6 - - + +
42I ALA* 3.9 17.5 - - + -
77I GLU 5.2 1.3 - - - +
78I MET* 3.6 18.8 - - - +
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Residues in contact with GLU 201 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196H LEU* 5.3 5.4 - - + -
197H GLU 3.1 15.1 + - - +
198H PRO* 3.9 10.3 - - + +
200H VAL* 1.3 80.8 - - - +
202H GLU* 1.3 59.8 + - - +
204H ARG* 3.5 15.9 + - - +
205H TYR* 3.2 23.7 + - - +
77I GLU* 4.9 6.0 + - - +
36J TYR* 3.1 35.9 + - - -
37J GLN* 4.9 9.9 - - - +
40J GLN* 4.2 13.7 - - - +
41J LYS* 6.0 1.4 - - - -
44J ARG* 5.0 18.5 + - - +
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Residues in contact with GLU 202 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198H PRO 2.8 19.7 + - - +
199H SER* 3.5 6.6 - - - +
201H GLU* 1.3 75.6 - - - +
203H ALA* 1.3 62.9 + - - +
205H TYR* 3.3 12.7 + - + +
206H ASN* 3.0 33.5 + - - +
34I GLU* 4.7 7.3 - - - +
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Residues in contact with ALA 203 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199H SER 3.3 8.3 + - - +
200H VAL 3.0 7.5 + - - +
202H GLU* 1.3 75.0 - - - +
204H ARG* 1.3 55.9 + - - +
205H TYR 2.9 5.2 - - - -
206H ASN* 2.8 24.5 + - - +
207H SER* 2.9 15.0 + - - -
34I GLU* 3.5 57.5 + - + +
35I GLU* 4.0 4.9 - - - +
38I ALA* 4.5 4.7 - - + -
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Residues in contact with ARG 204 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200H VAL* 2.9 27.9 + - - +
201H GLU* 3.5 16.8 + - - +
203H ALA* 1.3 77.1 - - - +
205H TYR* 1.3 58.5 + - - +
207H SER* 3.0 21.1 + - - +
208H CYS* 3.4 19.3 - - - -
35I GLU* 2.6 60.4 + - - +
39I ILE* 4.2 0.8 - - - +
77I GLU 3.0 27.7 + - - -
78I MET 3.3 15.4 + - - -
79I PHE* 3.3 24.2 + - - +
80I GLY* 3.4 7.3 - - - +
82I ASN* 5.4 0.9 - - - +
116I LYS* 4.2 8.5 - - - +
36J TYR* 2.7 43.2 + - + -
40J GLN* 4.6 0.2 + - - -
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Residues in contact with TYR 205 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201H GLU* 3.2 18.5 + - - +
202H GLU* 3.4 13.2 - - + +
203H ALA 2.9 0.8 - - - -
204H ARG* 1.3 79.3 - - - +
206H ASN* 1.3 64.9 - - - +
207H SER 3.4 0.4 - - - -
208H CYS* 4.0 9.0 - - + +
209H ARG* 3.0 42.9 + - - -
33J ALA* 4.0 30.5 - - + +
34J GLU* 5.6 1.3 - - - -
36J TYR* 5.5 6.7 - + + -
37J GLN* 3.3 32.9 + - + -
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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