Contacts of the helix formed by residues 257 - 265 (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 ARG 257 (chain P).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211P GLU* 3.4 35.7 + - + +
212P ILE* 4.1 1.7 - - + +
213P PRO* 3.6 26.6 - - - +
214P GLU* 3.0 27.1 + - - -
249P ALA* 2.7 43.8 + - - +
250P CYS 3.5 9.9 - - - +
251P ILE 3.6 0.2 - - - +
252P GLY* 3.6 13.8 - - - -
253P GLU 5.2 1.1 - - - +
256P SER* 1.3 82.4 - - - +
258P ILE* 1.3 59.7 + - - +
259P ALA 3.1 2.2 - - - +
260P ALA* 3.1 10.6 + - - +
261P ILE* 2.8 33.5 + - - +
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Residues in contact with ILE 258 (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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250P CYS 3.8 9.6 + - - +
251P ILE* 3.5 37.6 + - + +
255P GLY* 3.1 24.0 - - - +
256P SER 2.8 7.9 + - - -
257P ARG* 1.3 76.2 - - - +
259P ALA* 1.3 53.1 + - - +
261P ILE* 3.1 7.4 + - + +
262P LEU* 2.7 60.8 + - + +
270P LEU* 4.3 28.9 - - + +
272P VAL* 4.4 11.9 - - + -
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Residues in contact with ALA 259 (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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255P GLY 3.1 15.4 + - - +
256P SER* 4.3 7.9 - - - -
257P ARG 3.1 0.2 - - - -
258P ILE* 1.3 79.6 - - - +
260P ALA* 1.3 65.8 + - - +
262P LEU* 3.4 11.9 + - - +
263P LYS* 3.0 29.3 + - + +
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Residues in contact with ALA 260 (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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211P GLU* 3.2 32.9 - - + +
257P ARG* 3.1 16.0 + - - +
259P ALA* 1.3 80.4 - - - +
261P ILE* 1.3 63.5 + - - +
263P LYS* 3.1 16.0 + - - +
264P GLU* 3.4 11.1 + - - +
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Residues in contact with ILE 261 (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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204P VAL* 5.7 1.8 - - + +
207P LEU* 3.2 50.8 - - + +
208P MET* 4.0 10.3 - - + +
211P GLU* 3.5 20.0 - - + +
212P ILE* 5.5 5.4 - - + -
257P ARG 2.8 21.6 + - - +
258P ILE* 3.3 11.2 - - - +
260P ALA* 1.3 78.1 - - - +
262P LEU* 1.3 64.4 + - - +
263P LYS 3.0 0.9 + - - -
264P GLU* 3.1 12.3 + - - +
265P LEU* 3.4 23.7 + - + +
270P LEU* 3.6 30.3 - - + -
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Residues in contact with LEU 262 (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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258P ILE* 2.7 52.2 + - + +
259P ALA* 3.9 8.7 - - - +
261P ILE* 1.3 72.7 - - - +
263P LYS* 1.3 72.5 + - - +
265P LEU* 3.3 17.1 + - + +
266P LYS 3.6 6.2 + - - -
267P GLY 4.1 5.5 + - - -
268P GLU 4.0 15.1 - - - +
269P LYS* 4.6 1.8 - - - -
270P LEU* 3.9 33.4 - - + +
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Residues in contact with LYS 263 (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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259P ALA* 3.0 17.6 + - + +
260P ALA* 3.4 12.1 - - - +
261P ILE 3.0 0.6 + - - -
262P LEU* 1.3 86.5 + - - +
264P GLU* 1.3 61.5 + - - +
266P LYS* 3.3 24.0 + - - +
267P GLY* 5.3 3.2 - - - +
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Residues in contact with GLU 264 (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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167P ILE* 3.6 1.6 - - - +
177P LEU 4.8 2.4 - - - +
178P VAL* 3.7 5.4 - - - +
179P LYS* 2.7 56.9 + - + +
198P ARG* 2.8 43.8 + - - -
203P PHE* 3.9 7.1 - - + -
207P LEU* 3.7 21.8 - - + -
260P ALA 3.4 6.5 + - - +
261P ILE* 3.1 9.2 + - - +
263P LYS* 1.3 79.2 - - - +
265P LEU* 1.3 56.6 + - - +
266P LYS* 3.1 4.9 + - - +
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Residues in contact with LEU 265 (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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167P ILE* 3.8 14.0 - - + +
203P PHE* 3.9 22.2 - - + -
204P VAL* 4.2 16.4 - - + -
207P LEU* 4.0 7.2 - - + -
227P ARG* 3.7 26.9 - - - +
233P THR* 5.9 0.4 - - - +
261P ILE* 3.4 31.4 + - + +
262P LEU* 3.3 10.7 + - - +
263P LYS 3.1 1.4 - - - -
264P GLU* 1.3 75.2 - - - +
266P LYS* 1.3 57.1 + - - +
267P GLY 2.8 14.6 + - - -
268P GLU* 2.8 45.2 + - + +
269P LYS 4.9 1.3 - - - +
270P LEU* 4.7 13.7 - - + -
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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