Contacts of the strand formed by residues 186 - 197 (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 ARG 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A SER* 2.5 21.4 + - - -
27A VAL* 2.3 31.1 + - - +
28A ASP* 5.1 4.8 - - - +
29A PHE 5.8 0.2 - - - +
161A SER* 2.7 42.4 + - - +
162A VAL* 3.0 11.1 - - - +
163A PRO* 2.8 36.8 - - - +
164A LYS* 3.6 13.6 + - - +
179A PRO* 4.3 2.8 - - - +
180A ASP* 3.2 26.8 + - - +
184A PRO* 3.4 22.8 - - + +
185A SER* 1.3 81.6 + - - +
187A LYS* 1.3 59.5 + - - +
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Residues in contact with LYS 187 (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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160A VAL 3.5 0.7 - - - +
161A SER* 2.9 5.9 + - - -
162A VAL* 2.4 42.4 + - + +
164A LYS* 3.1 36.8 - - + +
166A LEU 4.4 0.4 - - - -
177A GLU* 2.5 35.3 + - + +
178A THR 4.0 8.7 - - - +
179A PRO* 4.9 8.5 - - + -
180A ASP 4.3 0.7 - - - +
186A ARG* 1.3 75.7 - - - +
188A ILE* 1.3 63.2 - - - +
189A TYR* 3.4 37.6 + - + +
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Residues in contact with ILE 188 (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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24A ARG* 5.9 2.7 - - + -
25A CYS 4.9 1.3 - - - +
159A GLU* 3.5 46.0 - - + +
160A VAL 3.7 7.4 - - - +
161A SER* 3.9 8.5 - - - +
176A GLY 4.2 0.2 - - - +
177A GLU* 3.7 2.8 - - - -
178A THR* 2.8 54.6 + - - +
179A PRO 4.0 1.3 - - - +
180A ASP* 3.3 37.7 - - + +
181A PRO* 4.7 1.8 - - + -
187A LYS* 1.3 74.5 - - - +
189A TYR* 1.3 61.5 + - - +
190A LYS* 4.0 9.2 + - + +
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Residues in contact with TYR 189 (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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158A ALA 3.6 0.2 - - - +
159A GLU* 3.0 4.9 - - - -
160A VAL* 2.5 45.5 + - - +
162A VAL* 3.6 22.7 - - + -
166A LEU 3.4 23.8 + - - -
167A VAL* 3.8 22.0 - - + +
168A ALA* 3.8 25.6 - - + -
174A ARG* 6.5 1.1 - - + -
176A GLY 4.0 2.9 - - - -
177A GLU* 3.6 32.1 + - + -
187A LYS* 3.4 40.6 + - + -
188A ILE* 1.3 71.8 - - - +
190A LYS* 1.3 60.8 + - - +
191A PHE* 3.7 19.9 - + + -
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Residues in contact with LYS 190 (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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158A ALA 3.4 2.0 - - - +
159A GLU* 3.9 33.2 - - + +
174A ARG* 3.5 1.9 - - - +
175A ASP* 2.7 44.6 + - + +
176A GLY* 2.9 36.8 + - - +
178A THR* 4.2 24.3 - - + +
188A ILE* 4.6 12.1 - - + +
189A TYR* 1.3 73.2 - - - +
191A PHE* 1.3 69.9 + - - +
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Residues in contact with PHE 191 (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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156A TYR* 5.1 1.1 - - + -
157A THR* 3.4 3.3 - - - -
158A ALA* 3.0 34.9 + - + +
160A VAL* 3.4 25.1 - - + -
168A ALA 3.1 30.5 - - - -
169A LEU* 3.7 8.3 - - - -
170A MET* 3.6 45.5 - - + -
172A ALA* 3.7 17.5 - - + -
173A ILE 3.0 9.0 - - - +
174A ARG* 3.9 26.9 - - + -
175A ASP 4.0 0.7 - - - +
189A TYR* 3.7 23.8 - + + -
190A LYS* 1.3 81.8 - - - +
192A ILE* 1.3 70.6 + - - +
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Residues in contact with ILE 192 (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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156A TYR 3.8 2.7 - - - -
157A THR* 3.7 18.6 - - + -
172A ALA* 3.6 2.5 - - - -
173A ILE* 2.8 61.4 + - + +
175A ASP* 3.8 28.5 - - + +
191A PHE* 1.3 81.7 - - - +
193A GLN* 1.3 61.6 + - - +
194A LYS* 3.9 42.2 - - + +
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Residues in contact with GLN 193 (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* 5.3 0.2 - - - -
155A THR* 3.3 9.5 - - - -
156A TYR* 2.8 65.8 + - + +
157A THR* 5.8 0.4 - - - -
171A SER 3.0 20.8 + - - +
172A ALA* 3.8 4.1 - - + +
173A ILE* 5.8 1.8 - - - +
192A ILE* 1.3 74.4 - - - +
194A LYS* 1.3 59.7 + - - +
195A VAL* 3.1 45.5 + - - +
197A ILE* 4.3 7.4 - - + -
253A TRP* 3.7 8.9 - - - +
273A PRO* 3.6 13.7 - - - +
274A CYS* 3.4 25.6 - - - -
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Residues in contact with LYS 194 (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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155A THR* 3.0 17.6 - - - +
173A ILE* 6.1 0.2 - - - +
192A ILE* 3.8 30.8 + - + +
193A GLN* 1.3 74.1 + - - +
195A VAL* 1.3 63.2 + - + +
196A PRO* 3.6 4.3 - - - +
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Residues in contact with VAL 195 (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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154A LEU 3.8 2.8 - - - +
155A THR* 3.8 2.1 - - - +
193A GLN* 3.1 19.7 + - - +
194A LYS* 1.3 79.7 - - + +
196A PRO* 1.3 70.5 - - + +
197A ILE* 3.3 12.1 + - - +
252A VAL* 4.0 22.9 - - + +
253A TRP* 3.4 43.7 - - + -
416A TYR* 3.5 33.4 - - + -
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Residues in contact with PRO 196 (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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153A LYS* 3.8 29.9 - - + +
154A LEU* 3.3 18.4 - - - +
155A THR* 3.7 6.7 - - + -
194A LYS 3.6 8.1 - - - +
195A VAL* 1.3 96.9 - - + +
197A ILE* 1.3 62.0 + - - +
253A TRP* 4.5 2.3 - - - -
304A ASN 4.6 3.5 - - - +
416A TYR* 4.3 25.8 - - + +
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Residues in contact with ILE 197 (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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153A LYS* 3.3 6.5 - - - -
154A LEU* 2.8 35.8 + - + +
156A TYR* 3.7 33.4 - - + -
193A GLN* 4.3 4.5 - - + -
195A VAL 3.4 15.7 - - - +
196A PRO* 1.3 76.2 - - - +
198A PRO* 1.4 83.2 - - + +
199A CYS* 3.7 1.0 + - - -
201A LEU* 4.1 17.3 - - + -
202A ILE* 4.3 10.1 - - + -
253A TRP* 3.5 30.5 - - + -
273A PRO* 4.0 12.6 - - + -
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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