Contacts of the helix formed by residues 151 - 164 (chain A) in PDB entry 3K8Y
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 151 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142A ILE* 4.4 3.2 - - - +
143A GLU 3.8 14.1 - - - -
144A THR* 3.5 12.7 - - - +
149A ARG 3.1 2.0 + - - -
150A GLN* 1.3 74.0 - - - +
152A VAL* 1.3 59.1 + - - +
153A GLU 3.6 1.3 - - - -
154A ASP* 3.4 23.9 + - - +
155A ALA* 2.9 25.6 + - - +
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Residues in contact with VAL 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 3.7 42.0 - - + +
22A GLN* 4.3 7.6 - - + -
23A LEU* 4.0 21.8 - - + +
144A THR* 4.4 4.5 - - - -
145A SER 3.5 25.1 - - - +
146A ALA* 4.2 5.2 - - - -
149A ARG* 3.2 22.4 + - + +
150A GLN 3.1 3.1 - - - +
151A GLY* 1.3 73.4 - - - +
153A GLU* 1.3 68.8 + - + +
155A ALA* 3.2 10.3 + - - +
156A PHE* 3.3 21.6 + - + -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23A LEU* 4.0 22.7 - - + +
149A ARG* 3.2 30.4 + - - +
152A VAL* 1.3 77.9 - - - +
154A ASP* 1.3 62.5 + - - +
156A PHE 3.3 1.2 + - - -
157A TYR* 2.8 64.1 + - + +
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Residues in contact with ASP 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A ILE* 4.3 10.5 - - + -
151A GLY* 3.4 23.7 + - - +
152A VAL 3.2 0.6 - - - -
153A GLU* 1.3 81.0 - - - +
155A ALA* 1.3 55.2 + - - +
157A TYR* 4.7 4.0 - - - -
158A THR* 2.7 40.3 + - - +
161A ARG* 5.7 2.2 - - - +
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Residues in contact with ALA 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 6.2 1.3 - - + -
79A LEU* 3.7 18.8 - - + +
112A VAL* 4.4 2.0 - - - +
114A VAL* 4.0 21.1 - - + -
142A ILE* 3.9 15.5 - - + +
144A THR* 3.9 17.3 - - + -
151A GLY 2.9 16.9 + - - +
152A VAL* 3.2 5.4 + - - +
154A ASP* 1.3 76.4 - - - +
156A PHE* 1.3 63.3 + - + +
158A THR* 3.4 2.6 + - - -
159A LEU 3.1 16.8 + - - -
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Residues in contact with PHE 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 22.6 - - + +
8A VAL* 3.9 20.2 - - + -
19A LEU* 3.9 25.8 - - + -
20A THR* 3.9 24.9 - - - -
23A LEU* 3.6 35.0 - - + -
53A LEU* 5.3 2.0 - - + -
55A ILE* 4.1 14.8 - - + -
79A LEU* 3.8 26.0 - - + -
152A VAL* 3.3 24.5 + - + +
153A GLU 3.3 5.2 + - - +
155A ALA* 1.3 79.7 - - + +
157A TYR* 1.3 68.7 + - + +
159A LEU* 3.2 9.0 + - + +
160A VAL* 3.1 24.2 + - - +
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Residues in contact with TYR 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A LEU* 4.7 13.5 - - + +
44A VAL* 4.1 19.6 - - + +
45A VAL 4.2 10.1 + - - -
46A ILE* 3.8 42.2 - - + +
53A LEU* 4.6 11.9 - - + -
153A GLU* 2.8 50.6 + - + +
154A ASP* 4.2 2.5 - - - +
156A PHE* 1.3 75.8 - - + +
158A THR* 1.3 66.6 + - - +
160A VAL* 3.2 8.7 + - - +
161A ARG* 3.0 53.6 + - - +
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Residues in contact with THR 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A VAL* 3.8 14.4 - - + -
140A PRO* 3.9 18.6 - - + -
142A ILE* 3.4 26.3 - - + +
154A ASP* 2.7 26.8 + - - +
155A ALA 3.7 2.2 - - - -
157A TYR* 1.3 78.1 - - - +
159A LEU* 1.3 56.8 + - - +
161A ARG* 3.1 19.3 + - + +
162A GLU* 2.9 29.5 + - + +
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Residues in contact with LEU 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 27.6 - - + -
77A GLY* 3.8 11.7 - - - +
78A PHE 3.7 47.8 - - - +
79A LEU* 3.7 16.8 - - + +
110A PRO* 3.9 5.8 - - + +
111A MET* 3.9 20.9 - - - +
112A VAL* 3.7 8.9 - - + +
155A ALA 3.1 13.5 + - - +
156A PHE* 3.2 10.7 + - + +
158A THR* 1.3 77.8 - - - +
160A VAL* 1.3 61.8 + - - +
162A GLU* 3.1 5.5 + - + +
163A ILE* 2.9 22.6 + - - +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.9 27.1 - - + -
6A LEU* 4.4 9.6 - - + -
46A ILE* 3.8 25.8 - - + -
53A LEU* 3.9 19.1 - - + -
156A PHE 3.1 14.6 + - - +
157A TYR 3.2 7.4 + - - +
159A LEU* 1.3 74.3 - - - +
161A ARG* 1.3 63.3 + - - +
163A ILE* 3.2 10.9 + - - +
164A ARG* 3.0 53.3 + - - +
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A ILE* 4.3 2.5 - - + +
47A ASP* 2.7 43.9 + - - +
154A ASP* 5.0 2.2 + - - +
157A TYR* 3.0 51.6 + - - +
158A THR* 3.1 19.8 + - + +
160A VAL* 1.3 75.1 - - - +
162A GLU* 1.3 61.8 + - + +
164A ARG* 3.6 18.3 + - - +
165A GLN* 3.1 32.7 + - - +
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Residues in contact with GLU 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A PRO* 4.1 11.2 - - + -
111A MET 4.0 19.9 + - - +
112A VAL* 4.0 8.7 - - + -
138A GLY 4.8 6.8 - - - +
139A ILE* 5.0 1.7 - - - +
140A PRO* 3.6 28.8 - - + +
158A THR* 2.9 19.7 + - - +
159A LEU* 3.1 10.1 + - + +
161A ARG* 1.3 75.1 - - - +
163A ILE* 1.3 59.9 + - - +
164A ARG 3.2 0.2 - - - -
165A GLN* 3.1 30.9 + - - +
166A HIS* 2.7 42.2 + - - -
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Residues in contact with ILE 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.9 28.5 - - + -
6A LEU* 3.4 33.4 - - + -
76A GLU* 3.9 24.2 - - + +
77A GLY* 3.9 15.7 - - - +
110A PRO* 3.7 23.3 - - + -
159A LEU 2.9 17.8 + - - +
160A VAL* 3.5 7.6 - - - +
162A GLU* 1.3 74.7 - - - +
164A ARG* 1.3 62.3 + - - +
166A HIS* 3.1 22.5 + - - +
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Residues in contact with ARG 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.0 26.9 + - + +
46A ILE* 3.0 34.1 + - - +
47A ASP* 2.9 34.3 + - - +
49A GLU* 3.0 26.6 + - - +
51A CYS* 4.8 0.6 - - - -
160A VAL* 3.0 31.8 + - - +
161A ARG* 3.8 16.3 - - - +
162A GLU 3.2 0.2 - - - -
163A ILE* 1.3 76.1 - - - +
165A GLN* 1.3 60.6 + - + +
166A HIS 3.3 5.4 + - - +
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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