Contacts of the helix formed by residues 158 - 167 (chain P) in PDB entry 3H1J
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 GLY 158 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P PHE 3.3 24.5 - - - -
152P SER* 4.2 2.5 - - - -
154P ILE* 3.4 18.0 + - - -
157P ILE* 1.3 81.8 - - - +
159P HIS* 1.3 54.5 + - - +
161P LEU* 2.4 41.5 + - - +
162P VAL* 3.1 3.3 + - - +
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Residues in contact with HIS 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152P SER* 4.1 24.7 + - - +
154P ILE 4.8 0.2 + - - -
156P TYR 5.2 3.6 - - - +
157P ILE 2.6 7.4 + - - +
158P GLY* 1.3 68.3 - - - -
160P THR* 1.3 55.9 + - - +
162P VAL* 2.5 34.9 + - - +
163P GLU* 3.0 11.2 + - - +
288P LYS* 5.4 4.0 + - - -
3104P UNL 3.8 21.7 + - - -
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Residues in contact with THR 160 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156P TYR 5.0 1.0 + - - -
157P ILE* 3.1 21.6 + - + -
159P HIS* 1.3 78.6 - - - +
161P LEU* 1.3 59.3 + - + +
163P GLU* 3.5 30.3 - - - +
164P TRP* 3.5 26.1 + - + +
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Residues in contact with LEU 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151P PHE* 4.7 16.6 - - + -
154P ILE* 3.8 22.2 - - + -
157P ILE* 3.6 32.3 - - + -
158P GLY* 2.4 33.5 + - - +
160P THR* 1.3 68.6 - - + +
162P VAL* 1.3 62.4 + - - +
164P TRP* 3.3 36.1 + - + +
165P ALA* 3.0 21.0 + - - +
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Residues in contact with VAL 162 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P THR 3.9 20.4 - - - +
149P ASN* 4.3 4.0 - - - +
151P PHE* 4.5 2.9 - - + -
152P SER* 4.0 24.2 - - - +
158P GLY 3.1 7.9 + - - +
159P HIS* 2.5 26.5 + - - +
161P LEU* 1.3 67.9 - - - +
163P GLU* 1.3 65.8 + - - +
165P ALA* 3.0 9.8 + - - +
166P TRP* 2.9 66.6 + - + +
3104P UNL 4.2 5.6 - - - +
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Residues in contact with GLU 163 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63E SER* 3.5 36.7 + - - -
64E ALA* 4.0 6.6 + - - +
159P HIS 3.0 8.5 + - - +
160P THR* 3.5 25.4 - - - +
162P VAL* 1.3 75.2 - - - +
164P TRP* 1.3 56.3 + - - +
166P TRP* 3.0 2.5 + - - -
167P GLY* 2.5 38.2 + - - -
168P GLY 3.4 15.4 + - - +
169P PHE* 3.3 35.3 - - + -
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Residues in contact with TRP 164 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59E ILE* 3.6 46.9 + - + +
62E LEU* 4.0 33.0 - - + -
63E SER* 3.9 20.8 + - - -
160P THR* 3.5 24.8 + - + +
161P LEU* 3.3 35.1 + - + +
162P VAL 3.2 0.6 - - - -
163P GLU* 1.3 82.4 + - - +
165P ALA* 1.3 65.0 + - - +
166P TRP 2.7 2.3 + - - -
167P GLY 2.9 1.2 + - - -
178P ARG* 2.7 30.5 + - - +
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Residues in contact with ALA 165 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148P THR* 3.8 29.2 - - + +
151P PHE* 6.2 1.3 - - + -
161P LEU 3.0 8.9 + - - +
162P VAL* 3.0 13.1 + - - +
164P TRP* 1.3 79.6 - - - +
166P TRP* 1.3 59.0 + - + +
175P THR* 3.3 16.6 - - - +
178P ARG* 3.7 6.8 - - - +
179P PHE* 3.4 12.8 - - - -
3001P SMA 4.7 16.4 - - + -
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Residues in contact with TRP 166 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94E LYS* 6.1 3.4 - - - -
144P ALA* 6.3 0.2 - - + -
145P THR* 4.0 8.3 - - + -
148P THR* 2.7 34.7 + - + +
149P ASN* 3.9 18.4 - - - -
162P VAL* 2.9 39.7 + - + +
163P GLU 3.8 0.2 - - - +
164P TRP 2.7 1.0 + - - -
165P ALA* 1.3 81.4 - - - +
167P GLY* 1.3 63.5 + - - +
168P GLY 2.9 13.8 + - - +
169P PHE* 3.8 7.2 - - - -
170P SER* 3.3 40.6 - - - +
171P VAL* 3.4 23.9 - - + +
174P PRO* 3.5 4.5 - - - +
175P THR* 2.7 50.7 + - + +
178P ARG* 4.2 3.1 - - - -
3104P UNL 3.8 15.9 - - - -
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Residues in contact with GLY 167 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62E LEU 3.2 10.8 - - - -
63E SER 4.1 1.0 - - - +
64E ALA* 3.3 21.8 - - - -
65E SER* 4.3 3.8 + - - -
68E VAL* 5.0 2.8 - - - +
163P GLU 2.5 15.4 + - - -
164P TRP 2.9 2.8 + - - -
166P TRP* 1.3 74.7 - - - +
168P GLY* 1.3 54.3 + - - -
174P PRO* 3.9 14.0 - - - +
178P ARG* 3.1 30.3 + - - -
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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