Contacts of the strand formed by residues 157 - 162 (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 157 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129P LYS* 3.9 29.4 - - + +
131P SER* 4.7 12.3 - - - +
153P ARG* 2.9 7.2 - - - +
154P ILE* 2.7 41.1 + - + +
155P GLY* 3.2 0.9 - - - -
156P LYS* 1.3 96.4 - - + +
158P GLU* 1.3 63.6 + - - +
185P VAL* 5.7 0.4 - - + -
192P PRO* 3.7 40.2 - - + +
193P LYS* 5.4 0.2 - - - -
194P ILE* 4.0 28.7 - - + -
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Residues in contact with GLU 158 (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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143P ILE* 3.3 30.4 - - + +
144P ARG* 5.8 3.1 + - - -
151P ASP* 4.7 11.0 - - + +
152P ILE 3.2 11.9 - - - +
153P ARG* 4.1 14.1 - - + -
157P LEU* 1.3 81.2 - - - +
159P THR* 1.3 65.4 + - - +
192P PRO 5.1 1.4 - - - +
193P LYS* 3.1 30.2 + - - +
194P ILE* 5.4 0.5 + - - +
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Residues in contact with THR 159 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151P ASP* 3.6 2.3 - - - -
152P ILE* 2.9 48.9 + - + +
154P ILE* 4.5 11.9 - - + -
158P GLU* 1.3 78.6 - - - +
160P ARG* 1.3 70.9 + - - +
193P LYS* 4.4 13.3 - - - +
194P ILE* 2.8 41.9 + - + +
195P LEU* 5.5 0.9 - - - +
196P VAL* 4.2 19.5 - - + -
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Residues in contact with ARG 160 (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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149P TRP* 3.1 42.4 - - + +
150P ALA 3.4 4.0 - - - -
151P ASP* 3.7 12.9 + - - +
159P THR* 1.3 84.0 + - - +
161P LEU* 1.3 60.5 + - - +
162P PRO* 3.4 14.2 - - + +
190P LYS* 5.2 11.5 - - - +
193P LYS* 5.9 10.0 - - - +
194P ILE 5.0 0.3 - - - +
195P LEU* 5.9 0.2 - - - -
196P VAL* 3.6 14.0 + - - +
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Residues in contact with LEU 161 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149P TRP* 4.0 0.7 - - - -
150P ALA* 2.7 33.3 + - + +
152P ILE* 4.1 21.8 - - + -
160P ARG* 1.3 72.5 - - - +
162P PRO* 1.3 77.8 - - + +
165P GLU* 4.1 16.2 - - + +
166P TRP* 3.0 39.7 + - + +
172P ILE* 5.7 5.6 - - + -
178P VAL* 4.5 8.5 - - + -
180P VAL* 4.0 22.0 - - + -
196P VAL* 4.1 16.2 - - + +
197P SER* 4.9 2.7 - - - -
198P ARG* 4.1 14.1 - - - -
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Residues in contact with PRO 162 (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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148P GLU 3.6 9.0 - - - +
149P TRP* 3.8 4.9 - - + -
160P ARG* 3.4 15.0 - - + +
161P LEU* 1.3 88.7 - - + +
163P LYS* 1.3 57.3 + - - +
164P LYS* 4.0 13.7 - - + +
165P GLU* 2.7 42.8 + - + +
166P TRP* 3.0 11.1 + - - -
196P VAL* 4.3 7.4 - - + +
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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
------------------------------------------------------------
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