Contacts of the helix formed by residues 262 - 279 (chain A) in PDB entry 5HNH
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 SER 262 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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259A ASP* 3.0 24.1 + - - +
261A THR* 1.3 79.5 + - - +
263A GLU* 1.3 58.9 + - - +
264A ASP* 3.3 8.1 + - - +
265A ASP* 3.1 26.1 + - - +
266A LYS* 2.9 34.7 + - - +
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Residues in contact with GLU 263 (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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261A THR 4.0 4.4 + - - +
262A SER* 1.3 72.6 + - - +
264A ASP* 1.3 66.4 + - - +
266A LYS* 2.9 35.3 + - - +
267A LYS* 3.3 31.4 + - + +
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Residues in contact with ASP 264 (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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262A SER* 3.2 6.6 + - - +
263A GLU* 1.3 80.7 - - - +
265A ASP* 1.3 62.5 + - - +
267A LYS* 3.2 12.3 + - - +
268A SER* 3.0 33.4 + - - +
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Residues in contact with ASP 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A LYS 4.3 4.0 - - - +
258A TYR* 3.4 18.8 - - + +
259A ASP* 2.7 52.0 + - - +
260A PHE* 5.7 0.2 - - - -
262A SER* 3.1 15.3 + - - +
264A ASP* 1.3 79.7 - - - +
266A LYS* 1.3 56.6 + - - +
268A SER* 4.4 6.1 + - - -
269A PHE* 3.0 29.6 + - - +
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Residues in contact with LYS 266 (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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122A LEU* 3.5 35.4 - - + +
260A PHE* 3.3 36.9 + - + +
261A THR* 4.8 1.8 - - - +
262A SER 2.9 21.6 + - - +
263A GLU* 2.9 43.7 + - - +
264A ASP 3.2 0.2 - - - -
265A ASP* 1.3 78.2 - - - +
267A LYS* 1.3 63.1 + - + +
269A PHE* 3.4 11.9 + - - +
270A PHE* 3.1 30.9 - - + -
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Residues in contact with LYS 267 (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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263A GLU* 3.3 17.7 - - + +
264A ASP* 3.2 13.7 + - - +
266A LYS* 1.3 78.3 - - + +
268A SER* 1.3 61.8 + - - +
270A PHE* 3.4 6.8 + - - +
271A LYS* 3.0 25.1 + - - +
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Residues in contact with SER 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258A TYR* 3.8 8.7 - - - -
264A ASP* 3.0 18.8 + - - +
265A ASP* 3.8 9.0 + - - -
266A LYS 3.3 0.2 - - - -
267A LYS* 1.3 74.5 - - - +
269A PHE* 1.3 57.0 + - - +
271A LYS* 4.4 6.5 - - - -
272A ASP* 2.6 51.4 + - - -
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Residues in contact with PHE 269 (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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117A ASN 3.4 25.6 - - - -
118A GLY* 3.6 19.7 - - - -
125A VAL* 3.7 21.8 - - + -
253A PHE* 3.7 22.2 - + - -
255A ALA* 3.9 19.1 - - + -
258A TYR* 3.4 29.3 - + + -
260A PHE* 3.8 24.0 - + + -
265A ASP 3.0 15.1 + - - +
266A LYS* 3.4 10.3 - - - +
268A SER* 1.3 76.2 - - - +
270A PHE* 1.3 84.0 + + - +
273A TRP* 2.8 31.2 + - - +
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Residues in contact with PHE 270 (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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75A LYS* 4.4 15.7 + - - +
118A GLY 3.3 20.9 - - - -
119A MET 5.3 0.2 - - - -
120A ASP 3.5 24.5 - - - -
121A LYS* 5.3 0.4 - - - -
122A LEU* 4.2 35.4 - - + -
125A VAL* 4.6 0.2 - - + -
266A LYS* 3.1 28.2 + - + -
267A LYS* 3.4 7.2 + - - +
268A SER 3.3 0.4 - - - -
269A PHE* 1.3 100.8 - + - +
271A LYS* 1.3 65.1 + - - +
273A TRP* 3.8 5.2 - - - +
274A GLN* 3.2 24.1 + - - +
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Residues in contact with LYS 271 (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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82A GLU 4.1 20.9 - - - +
83A ASP* 4.9 5.4 - - - +
84A ASP 4.8 11.3 - - - +
267A LYS 3.0 18.5 + - - +
268A SER* 3.7 5.8 - - - +
270A PHE* 1.3 75.4 - - - +
272A ASP* 1.3 69.8 + - - +
274A GLN* 3.4 6.1 + - - +
275A GLN* 3.1 23.7 + - + +
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Residues in contact with ASP 272 (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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253A PHE* 3.5 8.7 - - + -
257A LYS* 5.5 0.2 - - - -
258A TYR* 2.7 34.3 + - - +
268A SER* 2.6 33.9 + - - +
269A PHE 4.0 0.4 - - - +
271A LYS* 1.3 75.8 - - - +
273A TRP* 1.3 65.7 + - - +
275A GLN* 3.3 7.4 + - - +
276A TYR* 3.0 23.9 + - - +
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Residues in contact with TRP 273 (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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75A LYS* 5.1 1.3 + - + -
112A LYS 4.3 2.2 - - - -
114A GLN* 3.6 36.6 - - + -
117A ASN* 3.5 20.2 - - + -
118A GLY* 3.3 39.7 - - - +
119A MET* 3.7 25.7 - - + +
253A PHE* 3.4 30.4 - + + -
269A PHE 2.8 19.7 + - - +
270A PHE 3.8 4.7 - - - +
272A ASP* 1.3 76.5 - - - +
274A GLN* 1.3 72.5 + - - +
276A TYR* 3.1 24.0 + + - +
277A TYR* 2.9 68.5 + + + +
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Residues in contact with GLN 274 (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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74A GLY* 3.0 26.7 + - - +
75A LYS* 4.1 20.7 + - - +
78A GLY* 4.0 10.6 - - - -
80A PHE* 2.8 23.6 + - - +
81A TYR* 3.9 24.2 - - + -
82A GLU 5.4 0.4 - - - +
270A PHE 3.2 14.6 + - - +
271A LYS* 3.8 5.8 - - - +
273A TRP* 1.3 94.4 + - - +
275A GLN* 1.3 54.0 + - - +
277A TYR* 4.6 2.8 - - - +
278A SER* 2.7 42.5 + - - +
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Residues in contact with GLN 275 (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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81A TYR* 4.7 10.9 - - + -
271A LYS* 3.1 18.5 + - + +
272A ASP* 3.6 8.3 - - - +
274A GLN* 1.3 75.3 - - - +
276A TYR* 1.3 66.2 + - - +
279A ASN* 3.2 56.4 + - - +
280A VAL 5.2 6.1 + - - -
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Residues in contact with TYR 276 (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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111A PHE 4.6 1.2 + - - -
112A LYS* 2.7 69.7 + - + +
114A GLN* 3.8 14.2 + - - +
136A ARG* 5.7 1.4 + - - -
252A GLU* 3.7 35.2 + - + +
253A PHE* 3.9 17.9 - - + -
272A ASP 3.0 13.4 + - - +
273A TRP* 3.4 35.9 - + - +
275A GLN* 1.3 80.8 - - - +
277A TYR* 1.3 76.0 + - - +
279A ASN 3.8 1.2 - - - +
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Residues in contact with TYR 277 (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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75A LYS 3.4 24.7 - - - -
76A LEU 2.6 21.2 + - - -
78A GLY* 3.9 9.0 - - - -
92A ARG* 2.7 58.9 + - - -
109A ILE* 3.3 34.5 - - - +
112A LYS* 3.3 21.3 + - + +
113A PHE* 3.8 9.2 - - - -
119A MET* 3.3 19.9 - - + +
273A TRP* 2.9 50.3 + + + +
274A GLN* 4.2 4.9 - - - +
276A TYR* 1.3 83.1 - - + +
278A SER* 1.3 56.7 + - - +
279A ASN 3.6 0.2 - - - -
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Residues in contact with SER 278 (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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78A GLY* 3.3 31.4 - - - -
81A TYR* 4.2 6.8 - - - +
90A SER* 3.4 8.6 + - - -
91A GLY 3.2 0.7 + - - -
92A ARG* 3.0 33.7 + - - +
108A ASP* 5.8 0.2 - - - -
112A LYS* 4.6 1.3 - - - -
274A GLN* 2.7 29.1 + - - -
277A TYR* 1.3 77.2 - - - +
279A ASN* 1.3 78.8 + - - +
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Residues in contact with ASN 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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81A TYR* 3.5 27.0 - - - -
90A SER* 3.2 9.4 - - - -
91A GLY* 2.6 34.0 + - - +
112A LYS* 2.6 29.1 + - - -
275A GLN* 3.2 45.6 + - - +
276A TYR 3.8 4.5 - - - +
278A SER* 1.3 91.7 + - - +
280A VAL* 1.3 63.2 + - - +
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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