Contacts of the strand formed by residues 191 - 197 (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 GLY 191 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123P LYS* 3.4 18.3 - - - +
187P LYS* 2.9 16.3 - - - +
188P THR* 2.7 30.7 + - - +
189P THR 3.8 0.2 - - - -
190P LYS* 1.3 81.0 - - - +
192P PRO* 1.3 73.8 - - - +
193P LYS* 3.5 4.6 + - - +
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Residues in contact with PRO 192 (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* 3.8 17.5 - - + -
128P GLU 3.1 27.1 - - - +
129P LYS* 3.9 19.3 - - + +
157P LEU* 3.7 29.6 - - + +
158P GLU 5.1 0.9 - - - +
185P VAL* 4.4 9.4 - - + -
186P VAL 3.2 10.5 - - - +
187P LYS* 3.0 16.5 - - + +
191P GLY* 1.3 84.4 - - - +
193P LYS* 1.3 67.2 + - - +
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Residues in contact with LYS 193 (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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157P LEU* 5.4 0.2 - - - -
158P GLU* 3.1 35.4 + - - +
159P THR* 4.4 12.4 - - - +
160P ARG* 5.9 10.3 - - - +
185P VAL* 3.2 2.8 - - - -
186P VAL* 2.7 44.5 + - + +
188P THR* 4.3 14.6 - - + +
190P LYS* 4.1 39.4 - - + +
191P GLY 4.0 6.3 - - - +
192P PRO* 1.3 82.2 - - - +
194P ILE* 1.3 63.2 + - - +
195P LEU* 3.7 7.8 + - + +
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Residues in contact with ILE 194 (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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131P SER* 4.3 12.3 - - - +
133P LEU* 5.9 0.9 - - + -
154P ILE* 3.9 36.3 - - + -
157P LEU* 4.0 31.4 - - + -
158P GLU 5.4 0.2 + - - -
159P THR* 2.8 35.5 + - + +
160P ARG 5.0 0.5 - - - +
182P ILE* 3.3 49.1 - - + -
184P ASP 3.4 4.0 - - - +
185P VAL* 4.0 16.2 - - + +
193P LYS* 1.3 73.6 - - - +
195P LEU* 1.3 61.3 + - - +
196P VAL* 3.5 6.7 + - + +
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Residues in contact with LEU 195 (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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159P THR* 5.5 0.4 - - - +
160P ARG 5.9 0.4 - - - -
182P ILE* 3.5 5.2 - - - -
183P ILE* 2.8 40.2 + - + -
184P ASP* 2.6 39.9 + - + +
186P VAL* 4.4 22.7 - - + -
193P LYS* 3.9 17.5 - - + +
194P ILE* 1.3 75.9 - - - +
196P VAL* 1.3 59.0 + - - +
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Residues in contact with VAL 196 (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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152P ILE* 4.5 3.4 - - + -
154P ILE* 4.3 7.9 - - + -
159P THR* 4.2 11.2 - - + -
160P ARG 3.6 23.3 + - - +
161P LEU* 4.1 19.5 - - + +
162P PRO* 4.3 5.6 - - - +
165P GLU* 3.9 13.9 - - - +
180P VAL* 4.0 18.2 - - + -
181P TYR 3.2 6.5 - - - +
182P ILE* 3.4 31.2 - - + -
183P ILE* 4.0 5.3 - - - +
194P ILE* 3.8 10.3 - - + +
195P LEU* 1.3 74.4 - - - +
197P SER* 1.3 65.0 + - - +
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Residues in contact with SER 197 (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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161P LEU* 4.9 2.0 - - - -
165P GLU* 2.5 34.1 + - - +
180P VAL* 3.7 2.3 - - - -
181P TYR* 2.8 36.8 + - - +
183P ILE* 3.7 17.5 - - - -
196P VAL* 1.3 79.1 - - - +
198P ARG* 1.3 65.5 + - - +
199P ARG 3.1 11.1 + - - -
200P VAL* 3.5 17.6 + - - +
203P PHE* 5.1 0.2 - - - -
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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