Contacts of the helix formed by residues 278 - 290 (chain A) in PDB entry 2XH1
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 LYS 278 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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104A PRO* 3.9 28.5 - - + +
108A GLN* 2.8 47.7 + - + +
110A ASP* 3.5 36.0 + - + +
277A PRO* 1.3 72.0 - - - +
279A PRO* 1.3 65.3 - - + +
281A ILE* 3.8 0.7 - - - +
282A GLU* 2.8 40.9 + - + +
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Residues in contact with PRO 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASN* 5.5 3.8 - - - +
3A TYR* 3.8 29.6 - - + -
104A PRO* 3.3 28.0 - - + +
105A SER* 4.3 7.2 - - - -
107A GLY* 4.2 1.6 - - - -
277A PRO* 3.3 12.1 - - + -
278A LYS* 1.3 90.5 - - + +
280A LEU* 1.3 56.5 + - - +
282A GLU* 3.7 11.5 + - + +
283A ARG* 3.2 34.6 + - - -
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A TYR* 3.6 48.0 - - + +
6A PHE* 5.1 3.8 - - + -
7A ILE* 3.9 25.8 - - + -
127A MET* 3.6 16.9 - - + +
226A LEU* 4.2 14.6 - - + -
256A ILE* 3.7 27.6 - - + -
277A PRO* 3.1 23.2 + - + +
279A PRO* 1.3 76.7 - - - +
281A ILE* 1.3 66.5 + - + +
282A GLU 3.3 0.2 - - - -
283A ARG* 3.2 7.5 + - + +
284A VAL* 3.1 25.4 + - - +
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Residues in contact with ILE 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ASP* 3.9 17.7 - - + +
111A LEU 4.1 10.1 - - - +
112A CYS* 4.1 11.9 - - - -
256A ILE* 5.3 4.5 - - + -
274A LEU* 3.9 32.5 - - + +
275A THR 3.9 6.5 - - - -
276A GLY* 3.5 34.5 - - - +
277A PRO* 3.0 17.4 + - + +
278A LYS 3.8 3.6 - - - +
280A LEU* 1.3 77.0 - - - +
282A GLU* 1.3 56.4 + - - +
284A VAL* 3.2 6.9 + - + +
285A ILE* 2.8 44.9 + - + +
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 5.3 1.1 + - - +
278A LYS* 2.8 28.1 + - + +
279A PRO* 3.7 10.7 - - - +
281A ILE* 1.3 74.0 - - - +
283A ARG* 1.3 92.1 + - - +
285A ILE* 3.4 12.5 + - + +
286A LEU* 3.1 32.3 + - + +
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Residues in contact with ARG 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A ILE* 4.1 17.9 - - + +
11A SER* 3.0 43.9 + - - +
12A ALA* 3.4 12.1 + - - -
14A ARG* 2.7 37.4 + - - +
127A MET* 3.5 16.6 - - - -
279A PRO 3.2 19.2 + - - +
280A LEU* 3.2 9.7 + - + +
282A GLU* 1.3 105.6 + - - +
284A VAL* 1.3 61.8 + - - +
286A LEU* 3.4 21.6 + - - +
287A HIS* 3.3 20.6 + - - +
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Residues in contact with VAL 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112A CYS* 4.4 5.4 - - - -
114A THR* 5.1 1.3 - - + -
120A GLY* 5.0 0.9 - - - +
123A LYS* 4.0 19.3 - - + +
124A VAL* 3.9 32.5 - - + +
127A MET* 4.4 10.3 - - + -
274A LEU* 4.0 22.4 - - + -
280A LEU 3.1 14.6 + - - +
281A ILE* 3.2 8.9 + - - +
283A ARG* 1.3 72.9 - - - +
285A ILE* 1.3 66.6 + - - +
287A HIS* 3.1 7.7 + - - +
288A ILE* 2.9 40.7 + - + +
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Residues in contact with ILE 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER* 4.2 19.7 - - - -
78A ALA* 3.9 24.5 - - + +
110A ASP* 4.7 8.5 - - - +
111A LEU 4.8 1.6 - - - +
112A CYS* 3.9 22.2 - - + -
281A ILE* 2.8 36.4 + - + +
282A GLU* 3.7 10.5 - - + +
283A ARG 3.4 0.2 - - - -
284A VAL* 1.3 75.7 - - - +
286A LEU* 1.3 62.0 + - + +
288A ILE* 3.3 9.5 + - + +
289A GLN* 3.0 32.2 + - - +
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Residues in contact with LEU 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.8 27.0 - - + +
15A ASN 3.9 7.2 - - - +
16A PRO* 3.6 36.8 - - + -
282A GLU* 3.1 26.6 + - + +
283A ARG* 3.5 44.0 - - - +
284A VAL 3.2 0.4 - - - -
285A ILE* 1.3 80.6 - - + +
287A HIS* 1.3 63.2 + - - +
289A GLN* 3.4 28.5 + - - +
290A VAL* 3.6 13.0 + - - +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ARG* 3.4 41.4 + - - +
123A LYS* 3.5 32.7 + - + +
126A GLU* 3.3 33.1 + - + +
127A MET* 5.8 0.4 + - - -
283A ARG 3.3 8.0 + - - +
284A VAL* 3.1 10.6 + - - +
286A LEU* 1.3 77.0 - - - +
288A ILE* 1.3 65.2 + - - +
290A VAL* 3.1 18.0 + - + +
291A SER* 3.1 14.1 + - - -
122B CYS* 4.5 3.6 - - - -
126B GLU* 2.9 28.2 + - - -
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Residues in contact with ILE 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A SER* 3.8 17.0 - - - +
112A CYS* 4.4 7.9 - - + -
113A VAL 4.4 7.9 - - - +
114A THR* 4.0 22.7 - - + -
119A GLN* 4.1 13.5 - - - +
123A LYS* 3.4 20.8 - - + +
284A VAL* 2.9 32.0 + - + +
285A ILE* 3.6 11.0 - - - +
287A HIS* 1.3 75.7 - - - +
289A GLN* 1.3 60.6 + - - +
291A SER* 3.0 13.9 + - - -
292A THR* 3.3 13.6 + - - +
293A LEU 2.8 42.2 + - - +
294A HIS* 4.4 2.5 - - - +
295A PRO* 5.5 1.8 - - + -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ASN 5.0 0.5 - - - +
16A PRO* 4.4 1.0 - - - +
17A SER* 4.1 25.6 + - - -
77A SER* 3.2 34.6 + - - +
285A ILE* 3.0 16.6 + - - +
286A LEU* 3.4 33.3 - - - +
287A HIS 3.2 0.2 - - - -
288A ILE* 1.3 76.5 - - - +
290A VAL* 1.3 62.0 + - + +
293A LEU* 3.2 25.0 - - - +
118B GLN* 4.2 1.4 + - - -
147B GLN* 5.3 1.2 + - - -
1426B BF5 4.5 19.5 - - - -
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Residues in contact with VAL 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ARG* 3.9 23.8 - - - +
286A LEU 3.6 9.8 + - - +
287A HIS* 3.2 17.7 - - + +
289A GLN* 1.3 83.6 - - + +
291A SER* 1.3 58.5 + - - +
118B GLN* 3.5 20.7 - - - +
122B CYS* 3.4 19.0 - - - +
144B GLY* 4.3 5.6 - - - +
147B GLN* 3.8 33.9 - - + +
148B SER* 3.9 28.0 + - - +
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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