Contacts of the helix formed by residues 281 - 297 (chain A) in PDB entry 3HS3
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 ASN 281 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A ASP* 2.8 18.3 + - - +
280A GLN* 1.3 78.7 - - - +
282A PRO* 1.3 68.2 - - - +
283A LYS 3.2 3.1 - - - -
284A LEU* 3.0 25.3 + - + +
285A ILE* 3.0 18.0 + - - +
308A ILE* 4.1 5.6 - - + +
309A ASP* 2.9 32.0 + - - +
310A VAL* 4.5 0.4 - - - +
311A LEU* 4.1 28.0 - - - +
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Residues in contact with PRO 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A PHE* 3.5 39.5 - - + +
76A GLN* 3.6 37.0 - - + +
77A ILE* 3.5 13.6 - - + +
263A ASP 5.1 4.5 - - - +
279A ASP* 3.9 7.9 - - - +
280A GLN* 3.3 9.2 - - + +
281A ASN* 1.3 88.9 - - - +
283A LYS* 1.3 63.3 + - - +
285A ILE* 3.1 11.1 + - + +
286A GLY 2.9 18.5 + - - -
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Residues in contact with LYS 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A GLN* 3.5 20.3 + - + +
79A ASP* 4.5 15.1 + - - +
80A GLY* 3.6 11.6 - - - +
83A GLU* 3.5 21.4 + - - -
281A ASN 3.2 1.2 - - - -
282A PRO* 1.3 80.7 - - - +
284A LEU* 1.3 58.4 + - - +
286A GLY* 3.2 2.6 + - - -
287A GLN* 2.9 57.7 + - - +
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Residues in contact with LEU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 3.0 27.8 + - + +
283A LYS* 1.3 74.9 - - - +
285A ILE* 1.3 67.4 + - - +
287A GLN* 3.7 20.2 - - + +
288A THR* 2.8 42.6 + - - +
308A ILE* 3.7 25.1 - - + -
309A ASP* 5.4 3.1 - - + +
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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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73A PHE* 4.0 25.6 - - + -
77A ILE* 4.0 17.3 - - + -
140A TYR* 4.1 15.9 - - + -
141A ASP* 4.7 7.0 - - - +
152A ILE* 3.7 23.9 - - + +
154A SER* 4.2 19.3 - - - +
280A GLN 3.5 20.2 - - - +
281A ASN 3.0 15.3 + - - +
282A PRO* 3.1 9.6 + - + +
284A LEU* 1.3 76.6 - - - +
286A GLY* 1.3 59.1 + - - +
289A ALA* 3.0 27.4 + - - +
308A ILE* 4.1 18.6 - - + -
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Residues in contact with GLY 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ILE* 3.3 31.4 - - - +
81A ILE* 3.4 24.3 - - - +
282A PRO 2.9 10.9 + - - -
283A LYS 3.6 2.5 - - - -
285A ILE* 1.3 75.5 - - - +
287A GLN* 1.3 65.0 + - - +
289A ALA* 3.2 2.3 + - - +
290A ALA 3.1 17.3 + - - -
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLY* 3.6 23.7 - - - +
83A GLU* 2.7 25.6 + - - +
84A VAL* 3.8 13.2 - - + +
283A LYS* 2.9 37.0 + - - +
284A LEU* 3.7 27.2 + - + +
286A GLY* 1.3 74.6 - - - +
288A THR* 1.3 58.2 + - - +
290A ALA* 3.2 4.2 + - - +
291A HIS* 2.9 39.8 + - + +
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Residues in contact with THR 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152A ILE* 4.0 4.0 - - + -
284A LEU* 2.8 33.3 + - - +
285A ILE 3.9 2.9 - - - -
287A GLN* 1.3 75.6 - - - +
289A ALA* 1.3 65.9 + - - +
291A HIS* 3.8 8.7 - - + +
292A ARG* 2.8 28.7 + - + +
306A SER* 3.6 33.2 - - - +
308A ILE* 3.7 18.4 - - + +
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Residues in contact with ALA 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.7 1.8 - - + -
121A ILE* 4.1 27.6 - - + +
138A VAL* 4.0 8.5 - - + +
140A TYR* 4.6 7.4 - - + -
152A ILE* 3.6 24.4 - - + +
285A ILE 3.0 19.4 + - - +
286A GLY* 3.2 8.0 + - - +
288A THR* 1.3 74.9 - - - +
290A ALA* 1.3 57.2 + - - +
292A ARG* 4.0 1.6 - - - +
293A LEU* 3.0 29.6 + - - +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A ILE* 4.0 9.2 - - + +
84A VAL* 3.5 26.5 - - + -
85A ILE* 3.9 18.1 - - + +
121A ILE* 4.1 9.8 - - - +
286A GLY 3.1 12.6 + - - +
287A GLN 3.4 9.0 - - - +
289A ALA* 1.3 75.8 - - - +
291A HIS* 1.3 65.4 + - - +
293A LEU* 3.2 3.6 + - - +
294A LEU* 3.0 29.3 + - - +
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Residues in contact with HIS 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A VAL* 3.6 30.1 - - + +
287A GLN* 2.9 35.9 + - + +
288A THR* 3.2 9.2 + - + +
290A ALA* 1.3 76.9 - - - +
292A ARG* 1.3 65.1 + - + +
294A LEU* 3.2 13.2 + - + +
295A ASP* 3.0 30.4 + - - +
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Residues in contact with ARG 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138A VAL* 4.1 3.6 - - + -
150A VAL* 3.5 36.9 - - + +
151A ARG 4.8 0.2 + - - -
152A ILE* 3.8 9.0 - - + -
288A THR* 2.8 24.6 + - + +
289A ALA 4.0 3.1 - - - +
291A HIS* 1.3 78.5 - - + +
293A LEU* 1.3 61.2 + - - +
295A ASP* 3.3 19.5 + - - +
296A LEU* 3.1 26.2 + - - +
302A SER* 3.9 9.5 + - - -
304A ARG* 2.9 60.5 + - - +
306A SER* 2.8 44.8 + - - +
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.6 44.0 - - + -
85A ILE* 5.6 2.7 - - + -
119A GLY* 4.0 6.7 - - - -
120A ILE 3.8 12.1 - - - +
121A ILE* 3.6 16.2 - - + -
136A PRO* 3.6 34.8 - - + +
137A LEU 4.2 0.2 - - - +
138A VAL* 3.7 15.7 - - + +
289A ALA 3.0 19.6 + - - +
290A ALA* 3.6 5.4 - - - +
291A HIS 3.2 0.2 - - - -
292A ARG* 1.3 75.2 - - - +
294A LEU* 1.3 60.5 + - + +
296A LEU* 3.1 5.4 + - + +
297A MET* 2.9 38.4 + - - +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 5.8 1.1 - - + -
84A VAL* 4.0 24.5 - - + +
85A ILE* 5.2 8.3 - - + -
88A GLU* 4.3 18.4 - - + -
90A TYR* 3.9 34.8 - - + +
290A ALA 3.0 20.7 + - - +
291A HIS* 3.6 13.9 - - - +
293A LEU* 1.3 78.0 - - + +
295A ASP* 1.3 59.6 + - - +
297A MET* 3.3 15.6 + - + +
298A SER* 2.7 33.2 + - - +
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Residues in contact with ASP 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A HIS* 3.0 22.3 + - - +
292A ARG* 3.5 26.4 + - - +
293A LEU 3.1 0.2 - - - -
294A LEU* 1.3 78.8 - - - +
296A LEU* 1.3 57.5 + - + +
298A SER* 2.9 17.3 + - - -
300A ASN* 3.0 47.9 + - + +
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Residues in contact with LEU 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136A PRO* 4.0 18.6 - - + +
137A LEU 3.5 32.3 - - - +
138A VAL* 3.7 20.2 - - + -
150A VAL* 3.8 25.1 - - + -
292A ARG* 3.1 13.2 + - - +
293A LEU* 3.1 7.5 + - - +
295A ASP* 1.3 76.9 - - + +
297A MET* 1.3 58.4 + - - +
298A SER 3.0 4.2 + - - -
299A GLY* 3.2 12.3 + - - -
300A ASN 3.2 21.7 + - - +
301A ASN* 4.9 5.3 + - - +
302A SER 4.0 7.0 - - - +
303A THR* 6.1 0.9 - - + -
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Residues in contact with MET 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ILE* 3.9 10.5 - - + -
90A TYR* 3.2 35.7 - - + +
118A ASP* 3.5 44.2 - - + +
136A PRO* 4.0 17.7 - - + -
293A LEU* 2.9 39.3 + - - +
294A LEU* 3.6 14.1 - - + +
295A ASP 3.2 0.2 - - - -
296A LEU* 1.3 75.1 - - - +
298A SER* 1.3 57.6 + - - +
299A GLY 3.4 2.0 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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