Contacts of the strand formed by residues 265 - 274 (chain C) in PDB entry 1HHS
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 PHE 265 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88C ARG 3.0 6.7 + - - -
89C HIS* 3.1 16.3 - - + +
90C MET* 2.8 24.3 + - - -
211C ILE* 3.7 28.3 - - + -
220C PHE* 3.7 33.4 - - + -
221C VAL* 5.0 0.2 - - - -
222C SER* 3.7 33.0 - - - -
247C LYS* 3.5 20.9 - - + +
248C ASP* 4.8 5.8 - - - -
249C ALA* 4.1 7.0 - - - -
263C GLY* 3.6 25.4 - - - -
264C PHE* 1.3 79.4 - - - +
266C CYS* 1.3 69.4 + - - +
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Residues in contact with CYS 266 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 3.4 8.4 + - - -
90C MET* 4.8 2.5 - - - +
93C PHE* 3.3 21.1 - - - +
94C PRO 3.5 13.7 - - - +
95C MET* 3.7 7.2 - - - +
246C SER 5.3 0.4 - - - -
247C LYS* 2.8 31.5 + - - +
248C ASP 3.8 20.0 - - - -
249C ALA* 3.8 13.7 - - - -
251C ARG* 3.6 27.1 - - - -
252C LEU* 4.6 2.9 - - - -
265C PHE* 1.3 75.9 - - - +
267C GLU* 1.3 63.3 + - - +
268C ARG 3.9 0.2 + - - -
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Residues in contact with GLU 267 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 4.0 17.9 - - + -
90C MET 4.1 0.4 - - - +
91C ASN* 2.9 32.5 - - - +
92C GLY* 2.8 31.1 + - - -
93C PHE 2.9 16.7 + - - +
94C PRO* 3.5 5.2 - - + +
95C MET* 2.8 28.3 + - - +
205C ALA* 3.6 20.4 - - + +
206C GLN 4.2 4.7 - - - +
207C SER* 3.3 22.0 - - - +
266C CYS* 1.3 74.0 - - - +
268C ARG* 1.3 70.5 + - - +
269C ARG* 3.5 2.6 + - + +
528C PRO 5.0 0.9 - - - +
529C GLU 5.5 0.9 - - - +
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Residues in contact with ARG 268 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89C HIS* 5.1 1.4 + - - -
95C MET* 3.6 12.6 - - + -
205C ALA* 3.7 1.7 - - - -
206C GLN* 3.0 54.3 + - + +
209C ASP* 3.5 31.7 + - + +
225C ARG* 3.4 53.3 - - + +
247C LYS* 4.4 5.7 - - - +
266C CYS 3.9 1.2 + - - -
267C GLU* 1.3 76.2 - - - +
269C ARG* 1.3 70.8 + - - +
270C ARG* 2.7 48.2 - - + +
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Residues in contact with ARG 269 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C PHE* 3.9 21.2 - - - -
33C LYS 4.6 9.9 + - - -
94C PRO* 3.4 38.7 - - + +
95C MET* 3.6 27.5 + - + +
98C ALA* 4.4 17.8 - - + +
99C THR* 5.4 2.9 + - - +
203C TYR* 3.6 35.2 + - + +
204C ARG 3.5 19.1 - - - +
205C ALA* 4.3 8.3 - - + +
267C GLU* 3.5 5.5 + - + +
268C ARG* 1.3 82.6 + - - +
270C ARG* 1.3 64.7 + - - +
369C ALA 4.0 13.3 + - - -
370C PRO 4.4 6.1 + - - -
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Residues in contact with ARG 270 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C THR* 6.2 0.7 - - - -
203C TYR* 3.4 6.6 - - - -
204C ARG* 2.8 39.2 + - + +
206C GLN* 4.3 23.4 - - + +
268C ARG* 2.7 54.4 - - - +
269C ARG* 1.3 78.6 - - - +
271C THR* 1.3 69.0 + - - +
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Residues in contact with THR 271 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99C THR* 3.3 34.8 - - + +
101C PRO* 4.8 16.9 - - + +
201C VAL* 4.6 7.6 - - - -
203C TYR* 3.6 23.1 - - + -
270C ARG* 1.3 79.2 - - - +
272C ALA* 1.3 60.7 + - - +
273C MET* 5.2 6.5 - - - +
330C THR* 6.2 0.3 - - - +
393C SER* 4.7 3.6 + - - -
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Residues in contact with ALA 272 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201C VAL* 3.5 2.6 - - - +
202C VAL* 2.8 44.9 + - + +
204C ARG* 3.4 31.0 - - + +
271C THR* 1.3 76.2 - - - +
273C MET* 1.3 68.1 + - - +
393C SER* 3.4 12.3 - - - +
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Residues in contact with MET 273 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C PRO* 5.6 6.5 - - + -
199C TYR* 3.7 27.6 - - + -
200C TYR 3.4 4.9 - - - +
201C VAL* 3.8 22.4 - - + -
202C VAL* 5.2 2.2 - - - -
271C THR* 5.1 5.8 - - - +
272C ALA* 1.3 84.1 - - - +
274C GLY* 1.3 59.7 + - - +
365C VAL* 3.9 19.5 - - + -
389C VAL* 4.5 8.7 - - + -
392C SER* 3.5 36.1 - - - +
393C SER* 2.7 18.1 + - - +
394C GLY* 3.1 24.8 + - - +
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Residues in contact with GLY 274 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C CYS* 3.7 21.9 - - - +
198C ALA 4.5 0.2 - - - +
199C TYR* 3.4 4.2 - - - -
200C TYR* 2.9 37.9 + - - +
202C VAL* 5.3 2.9 - - - +
273C MET* 1.3 74.5 - - - +
275C GLY* 1.3 63.4 + - - -
394C GLY* 4.7 0.7 - - - -
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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