Contacts of the strand formed by residues 179 - 184 (chain I) in PDB entry 2HPC
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 179 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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203H ILE* 4.1 25.6 - - + -
204H PRO 6.0 0.7 - - - +
205H VAL* 5.3 5.0 + - - +
207H SER* 6.0 2.4 - - - -
226H LEU* 4.6 8.1 - - + -
145I ILE* 3.5 17.9 - - + -
166I LEU* 3.6 31.6 - - + -
167I TYR 4.0 11.9 - - - -
168I PHE* 3.2 39.0 - - + -
178I PHE* 1.3 88.0 - - - +
180I VAL* 1.3 63.6 + - - +
218I LEU* 3.0 39.5 - - + +
228I LEU* 4.5 2.3 - - - +
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Residues in contact with VAL 180 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I CYS* 3.5 23.3 - - - -
166I LEU* 3.1 24.4 - - - +
167I TYR 3.2 18.4 + - - +
169I ILE* 3.3 40.2 - - + -
178I PHE* 3.3 27.8 - - + -
179I LEU* 1.3 75.0 - - - +
181I TYR* 1.3 59.8 + - - +
182I CYS* 3.5 3.2 + - - -
192I THR* 5.1 7.2 - - - +
218I LEU* 4.4 4.0 - - - -
226I PHE* 6.3 0.4 - - - -
228I LEU* 4.6 6.5 - - + -
236I ILE* 5.3 4.3 - - + -
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Residues in contact with TYR 181 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153I CYS* 4.6 1.6 - - - -
164I SER* 4.4 7.3 + - - -
165I GLY 4.5 0.9 - - - -
166I LEU* 3.7 25.1 - - + -
180I VAL* 1.3 70.6 - - - +
182I CYS* 1.3 77.9 + - - +
183I GLU* 3.6 16.9 + - - +
192I THR* 4.8 2.6 + - - -
193I VAL* 3.6 37.3 + - + +
196I LYS* 4.8 9.8 + - + -
218I LEU* 4.5 12.1 - - + +
219I SER* 4.5 4.0 - - - +
220I PRO 4.1 1.6 - - - -
221I THR 2.8 30.3 + - - -
222I GLY* 3.5 20.6 - - - -
224I THR* 6.1 1.1 - - + -
226I PHE* 3.6 36.8 - + + -
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Residues in contact with CYS 182 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I CYS* 2.0 57.9 - - + -
156I ILE* 5.6 1.3 - - - -
164I SER* 3.9 7.2 - - - -
165I GLY 2.8 17.4 + - - +
167I TYR* 3.5 32.8 - - + -
169I ILE* 5.2 0.2 - - - -
180I VAL* 3.9 6.5 - - - -
181I TYR* 1.3 99.2 - - - +
183I GLU* 1.3 64.5 + - - +
184I ILE* 5.0 7.2 - - + -
191I TRP 3.8 3.1 - - - -
192I THR* 4.5 0.2 - - - +
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Residues in contact with GLU 183 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164I SER* 3.5 12.8 - - - -
181I TYR* 3.6 21.7 + - + +
182I CYS* 1.3 80.8 - - - +
184I ILE* 1.3 63.7 + - - +
191I TRP* 2.9 51.2 + - + -
192I THR* 5.0 0.7 - - - +
193I VAL* 5.0 3.8 - - + +
249I GLU* 4.6 5.4 - - - +
385I LYS* 3.7 30.4 + - + +
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Residues in contact with ILE 184 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153I CYS 5.1 0.2 - - - +
157I ALA* 3.3 31.0 - - + +
161I ALA* 3.2 35.4 - - + -
162I LYS* 3.5 30.5 - - + +
163I GLN 4.2 4.3 - - - +
164I SER* 3.8 15.1 - - - +
167I TYR* 4.3 10.8 - - + +
182I CYS* 5.0 5.6 - - + -
183I GLU* 1.3 83.8 - - - +
185I ASP* 1.3 85.1 + - - +
188I GLY* 5.2 2.7 - - - -
189I ASN 3.8 11.7 - - - +
190I GLY* 4.2 3.4 - - - -
191I TRP* 5.3 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