Contacts of the helix formed by residues 162 - 175 (chain H) in PDB entry 1LP9
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 162 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158H ALA 3.1 16.6 + - - -
159H TYR 3.3 0.4 + - - -
161H GLU* 1.3 78.0 - - - +
163H THR* 1.3 60.3 + - - +
164H CYS 3.4 0.7 - - - -
165H VAL* 3.2 3.6 + - - +
166H GLU* 2.9 37.8 + - - +
28L TYR* 3.7 15.7 - - - -
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Residues in contact with THR 163 (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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158H ALA 3.5 1.6 + - - -
159H TYR* 3.1 28.4 + - + -
162H GLY* 1.3 68.1 - - - -
164H CYS* 1.3 69.3 + - - +
166H GLU* 4.5 0.4 - - - +
167H TRP* 2.9 44.6 + - + +
1J ALA* 4.6 5.8 - - + +
28L TYR* 3.4 20.8 - - - +
98L SER* 3.4 26.9 - - - -
99L SER* 3.4 31.2 - - - -
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Residues in contact with CYS 164 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 3.4 28.7 - - - +
7H TYR* 6.4 0.2 - - - -
100H GLY* 3.9 9.9 - - - -
101H CYS* 2.1 54.1 - - - -
159H TYR* 2.7 40.6 + - + +
160H LEU* 3.6 7.9 - - - +
163H THR* 1.3 73.6 - - - +
165H VAL* 1.3 56.4 + - - +
168H LEU* 3.0 30.1 + - - +
1J ALA 5.4 0.2 - - - -
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Residues in contact with VAL 165 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101H CYS* 4.1 6.7 - - - -
103H VAL* 4.0 22.6 - - + +
109H PHE* 3.7 25.8 - - + +
160H LEU 3.5 17.9 + - - +
161H GLU 3.9 11.4 - - - +
162H GLY 3.2 7.7 + - - +
163H THR 3.2 0.4 - - - -
164H CYS* 1.3 76.0 - - - +
166H GLU* 1.3 67.4 + - + +
168H LEU* 3.3 4.7 + - - +
169H ARG* 3.0 62.1 + - - +
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Residues in contact with GLU 166 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162H GLY* 2.9 27.9 + - - +
163H THR 4.1 1.8 - - - +
165H VAL* 1.3 74.4 - - + +
167H TRP* 1.3 59.8 + - + +
169H ARG* 3.3 23.3 + - - +
170H ARG* 3.1 25.5 + - - +
27L THR* 4.9 10.4 - - - +
28L TYR* 3.9 31.7 + - - +
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Residues in contact with TRP 167 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5H MET* 4.4 1.3 - - + -
55H GLU* 4.1 2.7 - - - -
59H TYR* 3.6 31.9 - + + -
163H THR* 2.9 42.9 + - + +
164H CYS 4.3 1.6 - - - +
166H GLU* 1.3 75.3 - - + +
168H LEU* 1.3 66.9 + - - +
170H ARG* 3.2 57.5 + - - +
171H TYR* 2.9 50.3 + + + -
1J ALA* 3.6 30.7 - - + +
28L TYR* 3.6 17.8 + - - -
99L SER* 4.5 7.4 - - - -
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Residues in contact with LEU 168 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H HIS* 4.1 2.9 - - + +
4H SER* 3.7 41.5 - - - +
5H MET* 3.9 12.7 - - + +
28H VAL* 3.9 16.4 - - + -
101H CYS* 4.5 7.4 - - - +
103H VAL* 3.7 35.7 - - + -
164H CYS 3.0 19.6 + - - +
165H VAL 3.3 4.2 + - - +
167H TRP* 1.3 75.3 - - - +
169H ARG* 1.3 57.9 + - + +
171H TYR* 3.2 8.7 + - - +
172H LEU* 2.8 54.1 + - + +
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Residues in contact with ARG 169 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103H VAL* 5.9 2.2 - - + -
107H TRP* 3.0 57.4 + - + +
108H ARG* 4.1 12.5 - - - +
109H PHE 4.8 1.0 - - - +
165H VAL* 3.0 40.1 + - + +
166H GLU* 3.5 22.7 + - - +
167H TRP 3.2 0.2 - - - -
168H LEU* 1.3 77.7 - - + +
170H ARG* 1.3 57.0 + - - +
172H LEU* 3.4 11.0 + - + +
173H GLU* 3.0 37.1 + - - +
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Residues in contact with ARG 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55H GLU* 2.8 38.7 + - - -
166H GLU 3.1 13.9 + - - +
167H TRP* 3.3 49.7 - - - +
169H ARG* 1.3 76.4 - - - +
171H TYR* 1.3 58.3 + - - +
173H GLU* 3.3 7.1 + - - +
174H ASN* 2.9 46.8 + - - +
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Residues in contact with TYR 171 (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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5H MET* 3.5 31.0 - - - -
28H VAL* 3.9 17.0 - - + -
33H PHE* 3.8 10.5 - + - -
51H TRP* 3.6 21.7 - + + -
52H ILE* 3.4 26.5 - - + -
55H GLU* 4.2 11.0 - - - -
59H TYR* 2.7 30.1 + - - -
167H TRP* 2.9 43.6 + + - +
168H LEU* 3.6 4.3 - - - +
170H ARG* 1.3 75.9 - - - +
172H LEU* 1.3 65.5 + - - +
174H ASN* 4.5 2.9 - - - +
175H GLY* 2.9 21.1 + - - -
179H LEU* 3.4 8.9 - - - +
1J ALA 2.7 21.2 + - - -
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Residues in contact with LEU 172 (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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3H HIS* 3.6 53.8 - - + +
28H VAL* 4.1 20.2 - - + -
29H ASP* 4.3 0.2 - - - +
103H VAL* 4.9 1.8 - - + -
107H TRP* 3.8 32.1 - - + -
168H LEU* 2.8 34.4 + - + +
169H ARG* 3.6 6.3 - - + +
171H TYR* 1.3 75.1 - - - +
173H GLU* 1.3 62.1 + - - +
175H GLY 3.6 1.0 - - - -
176H LYS* 3.2 15.4 + - - -
179H LEU* 4.0 15.7 - - + -
180H GLN* 3.0 20.7 + - + +
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Residues in contact with GLU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107H TRP* 3.9 21.8 - - + -
169H ARG* 3.0 23.3 + - - +
170H ARG* 3.6 6.7 - - - +
172H LEU* 1.3 74.9 - - - +
174H ASN* 1.3 68.6 + - - +
176H LYS* 3.2 18.9 + - - +
180H GLN* 4.2 5.6 - - - +
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Residues in contact with ASN 174 (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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51H TRP* 3.9 12.4 - - + +
54H GLN* 3.6 42.9 + - - +
55H GLU* 3.6 23.0 + - - -
170H ARG* 2.9 39.1 + - - +
171H TYR* 4.1 5.2 - - + +
173H GLU* 1.3 77.4 - - - +
175H GLY* 1.3 57.9 + - - +
176H LYS 3.4 1.8 + - - -
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Residues in contact with GLY 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51H TRP* 3.5 29.5 - - - +
171H TYR 2.9 13.6 + - - -
172H LEU 3.6 4.3 - - - -
174H ASN* 1.3 75.8 - - - +
176H LYS* 1.3 55.2 + - - +
177H GLU* 3.3 3.1 - - - -
178H THR* 3.0 7.8 + - - -
179H LEU* 2.8 34.7 + - - +
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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
------------------------------------------------------------
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