Contacts of the strand formed by residues 177 - 188 (chain P) in PDB entry 1HH2
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 177 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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139P THR* 4.0 19.3 - - + -
140P ALA 3.4 7.0 - - - +
141P GLU* 3.9 28.5 - - + -
175P GLY 4.2 7.4 - - - +
176P ASP* 1.3 76.3 - - - +
178P VAL* 1.3 63.4 + - - +
264P GLU* 4.8 3.3 - - - +
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Residues in contact with VAL 178 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139P THR* 3.4 5.0 - - - -
140P ALA* 2.9 38.1 + - + +
142P VAL* 3.8 25.1 - - + -
152P ILE* 4.8 2.2 - - + -
161P LEU* 4.5 11.4 - - + -
172P ILE* 3.7 28.9 - - + -
176P ASP* 4.4 6.5 - - + -
177P LEU* 1.3 79.2 - - - +
179P LYS* 1.3 61.9 + - - +
180P VAL* 4.1 16.6 - - + -
198P ARG* 3.8 15.3 - - - +
264P GLU* 3.8 3.6 - - - +
266P LYS* 4.5 7.9 - - - +
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Residues in contact with LYS 179 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137P VAL* 3.4 18.4 - - + -
138P THR 3.4 3.1 - - - +
139P THR* 2.9 33.0 - - + +
178P VAL* 1.3 74.3 - - - +
180P VAL* 1.3 61.1 + - - +
198P ARG* 2.7 28.8 + - - +
203P PHE* 3.5 9.2 - - + -
207P LEU* 3.8 11.0 - - + +
210P LEU* 3.0 30.0 - - - +
211P GLU* 5.3 5.7 + - - -
264P GLU* 2.7 38.1 + - + +
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Residues in contact with VAL 180 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136P THR 3.8 0.5 - - - +
137P VAL* 3.2 7.2 - - - +
138P THR* 3.0 49.7 + - + +
140P ALA* 4.2 14.1 - - + -
152P ILE* 4.1 11.9 - - + -
154P ILE* 4.3 1.6 - - + -
161P LEU* 4.0 29.2 - - + -
178P VAL* 4.1 8.1 - - + -
179P LYS* 1.3 82.0 - - - +
181P TYR* 1.3 60.9 + - - +
182P ILE* 3.9 0.6 + - + -
196P VAL* 4.0 24.9 - - + -
197P SER 3.8 5.4 - - - +
198P ARG* 4.0 5.4 - - + -
203P PHE* 3.9 1.3 - - - -
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Residues in contact with TYR 181 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135P GLY* 3.4 41.7 + - - -
136P THR 3.5 14.4 - - - -
137P VAL* 4.2 6.1 - - + -
180P VAL* 1.3 73.6 - - - +
182P ILE* 1.3 72.4 + - - +
183P ILE* 3.5 19.0 + - + -
196P VAL* 3.2 6.9 - - - -
197P SER 2.8 37.8 + - - +
200P VAL* 3.8 14.8 - - + -
202P GLU* 3.3 48.3 - - + +
203P PHE* 3.8 22.7 - - + -
206P GLY* 5.4 0.9 - - - -
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Residues in contact with ILE 182 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133P LEU* 3.5 30.1 - - + +
134P LYS* 3.9 13.7 - - - -
135P GLY 2.8 28.2 + - - -
136P THR 2.8 18.3 + - - +
138P THR* 4.1 22.9 - - + -
154P ILE* 4.1 3.6 - - + -
180P VAL* 4.4 1.8 - - + +
181P TYR* 1.3 78.7 - - - +
183P ILE* 1.3 59.7 + - - +
184P ASP 3.7 11.7 - - - +
185P VAL* 3.9 7.6 - - + -
194P ILE* 3.3 38.4 - - + -
195P LEU 3.5 1.1 - - - -
196P VAL* 3.4 16.6 - - + -
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Residues in contact with ILE 183 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134P LYS* 4.0 12.3 - - - +
135P GLY 4.9 0.3 + - - -
165P GLU* 5.1 4.5 - - - +
181P TYR* 3.9 27.5 + - + +
182P ILE* 1.3 75.7 - - - +
184P ASP* 1.3 68.6 + - + +
195P LEU* 2.8 21.2 + - + +
196P VAL 4.0 11.9 - - - +
197P SER* 3.7 26.0 - - - -
200P VAL* 4.8 10.5 - - + -
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Residues in contact with ASP 184 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P GLU* 3.2 2.4 - - - +
134P LYS* 3.0 36.2 + - - +
182P ILE* 3.4 1.4 - - - -
183P ILE* 1.3 85.1 - - + +
185P VAL* 1.3 93.6 + - - +
186P VAL* 4.0 12.8 - - - +
193P LYS 4.5 0.2 - - - -
194P ILE* 3.4 2.3 - - - +
195P LEU* 2.6 51.6 + - + +
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Residues in contact with VAL 185 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P GLU* 4.4 4.6 - - + +
129P LYS* 4.9 4.9 - - + -
131P SER* 3.7 12.8 - - - +
132P GLU* 2.4 66.0 + - + +
134P LYS* 4.2 2.0 - - + +
157P LEU* 5.7 0.4 - - + -
182P ILE* 3.9 15.7 - - + -
184P ASP* 1.3 91.8 + - - +
186P VAL* 1.3 64.4 + - - +
187P LYS 4.3 0.3 + - - -
192P PRO* 4.4 19.3 - - + -
193P LYS 3.2 9.4 - - - +
194P ILE* 4.0 18.2 - - + -
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Residues in contact with VAL 186 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128P GLU* 4.7 0.7 - - - -
184P ASP* 4.0 18.8 - - - +
185P VAL* 1.3 78.6 - - - +
187P LYS* 1.3 60.2 + - - +
188P THR* 3.3 21.9 + - + +
192P PRO* 3.2 4.0 - - - +
193P LYS* 2.7 48.6 + - + +
195P LEU* 4.4 24.0 - - + -
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Residues in contact with LYS 187 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123P LYS* 3.5 26.2 - - - +
125P LYS* 4.3 13.9 - - - +
126P GLN 5.2 2.0 - - - +
127P PHE 2.7 28.9 - - - +
128P GLU* 3.2 36.2 - - + +
186P VAL* 1.3 70.9 - - - +
188P THR* 1.3 73.3 + - - +
191P GLY* 2.9 40.6 + - - +
192P PRO* 3.6 8.7 - - - -
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Residues in contact with THR 188 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186P VAL* 3.7 29.4 - - + +
187P LYS* 1.3 93.7 + - - +
189P THR* 1.3 61.2 - - - +
190P LYS* 2.9 21.9 + - - +
191P GLY 2.7 21.8 + - - +
193P LYS* 4.3 14.0 - - + +
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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