Contacts of the strand formed by residues 154 - 163 (chain A) in PDB entry 1HS6
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 LEU 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A THR* 3.7 20.9 - - + +
19A LYS 3.4 22.9 - - - +
20A HIS 3.7 1.8 - - - +
21A LEU* 3.7 28.5 - - + +
40A LEU* 5.8 0.7 - - + -
147A GLN 5.9 1.1 - - - +
152A VAL* 4.3 13.5 - - + +
153A LYS* 1.3 78.9 - - - +
155A THR* 1.3 74.9 - - - +
156A TYR* 4.6 4.9 - - + -
196A PRO* 3.3 8.2 - - - +
197A ILE* 2.8 43.8 + - + +
199A CYS* 4.6 17.3 - - + +
202A ILE* 4.9 10.3 - - + -
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Residues in contact with THR 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 LYS 3.0 11.1 + - - +
20A HIS* 2.7 26.0 + - - +
21A LEU 2.9 20.8 + - - -
154A LEU* 1.3 79.7 - - - +
156A TYR* 1.3 66.4 + - - +
193A GLN 3.3 7.0 - - - -
194A LYS* 3.0 35.4 - - - +
195A VAL 4.3 1.1 - - - -
196A PRO* 3.7 18.6 - - + +
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Residues in contact with TYR 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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20A HIS* 3.5 4.0 - - - -
21A LEU* 3.0 33.9 - - + +
23A LEU* 5.7 0.2 - - + -
154A LEU* 4.6 2.9 - - + -
155A THR* 1.3 80.9 - - - +
157A THR* 1.3 77.6 + - - +
158A ALA* 4.3 10.3 - - + -
170A MET* 3.7 26.3 - - + +
171A SER* 2.9 41.8 + - - -
172A ALA* 3.5 13.3 - - + +
191A PHE* 5.1 0.9 - - + -
193A GLN* 2.8 54.1 + - + +
197A ILE* 3.7 27.8 - - + -
202A ILE* 4.2 17.0 - - + -
203A ALA 4.7 0.2 + - - -
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Residues in contact with THR 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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20A HIS* 3.1 22.5 + - + -
21A LEU 2.8 4.6 + - - +
22A HIS* 3.2 21.2 - - - +
23A LEU* 2.7 25.3 + - - +
156A TYR* 1.3 84.7 - - - +
158A ALA* 1.3 63.0 + - - +
159A GLU* 5.8 1.1 - - - -
191A PHE 3.4 4.7 - - - -
192A ILE* 3.7 28.7 - - + -
193A GLN 4.6 0.7 - - - +
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Residues in contact with ALA 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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23A LEU* 2.8 27.1 - - + +
156A TYR* 4.3 8.7 - - + -
157A THR* 1.3 77.7 - - - +
159A GLU* 1.3 69.7 + - - +
160A VAL* 4.2 0.4 - - + -
170A MET* 3.8 28.5 - - + -
189A TYR 3.6 0.6 - - - +
190A LYS* 3.4 4.7 - - - +
191A PHE* 3.0 36.6 + - + +
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Residues in contact with GLU 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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22A HIS* 3.4 20.1 + - - +
23A LEU 2.6 9.2 + - - +
24A ARG* 3.1 37.8 - - + -
25A CYS* 3.0 25.3 + - - +
157A THR* 5.8 1.0 - - - -
158A ALA* 1.3 75.5 + - - +
160A VAL* 1.3 63.8 + - - +
188A ILE* 3.5 21.7 - - + +
189A TYR 3.0 6.3 - - - +
190A LYS* 3.9 25.2 - - + +
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A CYS* 3.1 18.6 - - - +
27A VAL* 3.8 17.3 - - + -
158A ALA* 5.1 0.4 - - + -
159A GLU* 1.3 80.2 - - - +
161A SER* 1.3 60.6 + - - +
162A VAL* 3.7 22.9 + - + -
168A ALA* 4.3 5.8 - - + -
170A MET* 4.2 14.1 - - - -
187A LYS 3.5 1.0 - - - +
188A ILE* 3.5 3.5 - - - +
189A TYR* 2.5 44.5 + - + +
191A PHE* 3.4 33.0 - - + -
204A LEU* 4.4 10.5 - - + -
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Residues in contact with SER 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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25A CYS 2.7 11.8 + - - -
26A SER* 2.6 35.0 + - - -
27A VAL 2.9 11.8 + - - -
160A VAL* 1.3 72.7 - - - +
162A VAL* 1.3 56.4 + - - +
180A ASP* 3.0 17.8 + - - -
186A ARG* 2.7 39.4 + - - +
187A LYS 2.9 8.0 + - - -
188A ILE* 3.9 11.5 - - - +
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Residues in contact with VAL 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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27A VAL* 4.0 9.9 - - + -
160A VAL* 3.7 20.6 + - + +
161A SER* 1.3 79.8 + - - +
163A PRO* 1.3 72.3 - - + +
166A LEU* 3.4 29.4 - - + +
168A ALA* 4.0 8.7 - - + -
186A ARG* 3.1 5.6 - - - +
187A LYS* 2.4 42.6 + - + -
189A TYR* 3.6 22.7 - - + -
206A VAL* 3.8 23.8 - - + -
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Residues in contact with PRO 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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27A VAL 3.9 2.7 - - - +
29A PHE* 4.3 13.9 - - + +
162A VAL* 1.3 82.1 - - + -
164A LYS* 1.3 56.7 + - - +
165A GLU* 3.0 25.1 - - - +
166A LEU* 2.6 53.0 + - + +
185A SER 3.4 11.0 - - - +
186A ARG* 2.8 35.0 - - - +
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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