Contacts of the helix formed by residues 159 - 170 (chain K) in PDB entry 3A68
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 ASP 159 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40K LYS 3.4 12.7 - - - +
41K TYR* 3.4 14.7 - - - -
42K VAL 4.9 0.2 + - - -
45K SER* 4.1 14.4 + - - +
105K ARG* 2.9 43.9 + - - -
154K ALA* 2.8 20.3 + - - +
155K THR* 5.7 0.4 - - - -
157K ASN* 3.3 3.1 - - + +
158K GLY* 1.3 68.5 - - - +
160K VAL* 1.3 63.3 + - - +
161K GLN* 3.5 3.5 + - - +
162K LEU* 3.0 20.0 + - + -
163K ALA* 3.2 22.5 + - - +
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Residues in contact with VAL 160 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K GLY* 3.3 11.3 + - - +
159K ASP* 1.3 73.6 + - - +
161K GLN* 1.3 58.1 + - - +
163K ALA* 3.5 5.4 + - - +
164K ASP* 3.0 25.5 + - - +
148P LEU* 4.0 22.5 - - + +
151P HIS* 3.5 41.1 - - + +
167P GLU* 3.9 8.4 - - + +
171P LEU* 3.4 24.7 - - + -
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Residues in contact with GLN 161 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101K TYR* 2.5 34.0 + - - -
105K ARG* 3.7 9.7 + - - +
159K ASP* 3.4 2.0 + - - +
160K VAL* 1.3 78.6 - - - +
162K LEU* 1.3 60.6 + - - +
164K ASP* 3.3 9.8 + - + +
165K PHE* 2.9 40.2 + - - +
148P LEU* 5.2 3.7 - - + +
171P LEU* 3.7 37.7 - - + +
172P GLY* 3.7 17.2 - - - -
175P VAL* 3.6 25.6 - - + +
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Residues in contact with LEU 162 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41K TYR* 4.4 2.5 - - + -
45K SER* 3.7 32.5 - - - +
49K VAL* 4.0 22.0 - - + -
98K LEU* 6.1 0.2 - - + -
101K TYR* 3.3 36.0 + - + +
105K ARG* 3.9 1.6 - - - +
150K LEU* 4.6 10.8 - - + -
153K VAL* 6.0 0.2 - - + -
154K ALA* 3.7 20.9 - - + +
159K ASP* 3.0 23.7 + - + +
161K GLN* 1.3 73.8 - - - +
163K ALA* 1.3 67.3 + - - +
165K PHE* 3.2 4.5 + - + +
166K VAL* 3.1 35.5 + - + +
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Residues in contact with ALA 163 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K HIS* 3.3 38.5 - - + +
154K ALA* 3.7 13.4 - - + +
155K THR* 4.3 8.3 - - + -
159K ASP 3.2 16.6 + - - +
160K VAL* 3.7 5.8 - - - +
162K LEU* 1.3 80.9 - - - +
164K ASP* 1.3 61.9 + - - +
166K VAL* 3.3 2.1 + - - +
167K GLU* 3.1 21.0 + - - +
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Residues in contact with ASP 164 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160K VAL 3.0 17.4 + - - +
161K GLN* 3.6 14.9 + - + +
162K LEU 3.2 0.2 - - - -
163K ALA* 1.3 77.4 - - - +
165K PHE* 1.3 57.1 + - - +
167K GLU* 3.2 24.0 - - - +
168K THR* 2.9 46.1 + - - -
373K CA 3.9 4.0 - - - -
167P GLU* 3.6 45.7 - - + +
168P THR* 4.5 5.2 + - - -
171P LEU* 5.9 0.7 - - + -
172P GLY* 5.3 2.1 + - - -
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Residues in contact with PHE 165 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97K LYS* 4.2 17.0 - - + -
98K LEU* 3.8 15.0 - - + -
101K TYR* 3.6 60.8 - + + -
104K LYS* 6.1 3.1 - - - -
161K GLN* 2.9 24.5 + - - +
162K LEU* 3.2 4.9 + - + +
164K ASP* 1.3 77.0 - - - +
166K VAL* 1.3 66.9 + - + +
168K THR* 4.7 3.1 - - - -
169K GLU* 2.8 59.4 + - + +
170K TYR* 3.6 28.9 - + - -
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Residues in contact with VAL 166 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K LEU* 3.7 34.5 - - + +
150K LEU* 3.7 29.6 - - + -
151K HIS* 4.3 12.8 - - + +
162K LEU* 3.1 23.7 + - + +
163K ALA* 3.8 6.7 - - - +
165K PHE* 1.3 84.5 - - + +
167K GLU* 1.3 59.0 + - - +
170K TYR* 3.0 30.7 + - + +
171K LEU* 3.2 21.5 + - + -
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Residues in contact with GLU 167 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151K HIS* 3.2 18.8 + - + -
163K ALA* 3.1 13.3 + - - +
164K ASP* 3.2 25.7 - - - +
166K VAL* 1.3 77.6 - - - +
168K THR* 1.3 65.8 + - - +
171K LEU* 3.7 36.3 + - + +
172K GLY 4.1 4.9 + - - -
371K CA 2.9 24.6 - - - -
373K CA 2.6 25.8 - - - -
167P GLU* 4.0 2.1 - - - +
160U VAL* 3.7 8.2 - - + +
164U ASP* 3.6 31.0 - - + +
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Residues in contact with THR 168 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164K ASP* 2.9 36.7 + - - -
165K PHE* 4.0 3.4 - - - -
167K GLU* 1.3 79.6 - - - +
169K GLU* 1.3 73.5 + - + +
173K GLU* 3.8 1.2 - - - +
215K CA 2.6 28.2 - - - -
164U ASP* 4.7 6.3 + - - -
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Residues in contact with GLU 169 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94K HIS* 6.0 0.5 - - - -
97K LYS* 3.2 33.0 + - - +
165K PHE* 2.8 42.1 + - + +
168K THR* 1.3 90.9 - - - +
170K TYR* 1.3 76.6 + - + +
173K GLU* 3.3 20.5 - - - +
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Residues in contact with TYR 170 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56K GLU* 4.5 5.2 - - - -
94K HIS* 2.7 52.0 + + + -
97K LYS* 3.3 27.2 - - - +
98K LEU* 3.2 23.7 + - + +
147K LEU* 3.9 34.0 - - + +
165K PHE* 3.6 28.5 - + - -
166K VAL* 3.0 23.9 + - + +
169K GLU* 1.3 90.9 - - + +
171K LEU* 1.3 62.3 + - - +
172K GLY 3.5 1.8 - - - -
173K GLU* 3.4 8.1 + - + +
174K GLN* 2.9 30.4 + - - +
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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