Contacts of the helix formed by residues 281 - 293 (chain A) in PDB entry 3TMP
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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176A ASN* 5.9 0.8 - - - +
177A SEP 3.1 31.1 + - - +
180A GLU* 2.8 28.4 + - - +
225A LEU* 4.1 1.2 - - - +
269A TYR* 5.1 1.3 - - - +
273A LYS* 3.8 0.2 - - - +
280A GLY* 1.3 73.0 - - - +
282A HIS* 1.3 80.1 + - - +
283A ILE* 3.3 5.8 - - + +
284A GLU* 2.8 26.0 + - - +
285A MET* 3.1 20.6 + - - +
42B ARG* 5.2 1.8 - - - +
70B VAL* 6.2 0.7 - - - -
71B LEU 3.9 3.9 - - - +
73B LEU 2.9 15.9 + - - -
74B ARG* 2.8 26.7 + - - +
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Residues in contact with HIS 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281A ASN* 1.3 78.9 + - - +
283A ILE* 1.3 64.0 + - - +
285A MET* 3.1 13.6 + - - +
286A GLN* 3.0 23.7 + - + +
314A PHE* 3.3 37.3 - + - -
8B LEU* 3.8 32.8 - - + +
9B THR* 3.8 10.4 + - + +
69B LEU 4.9 0.9 - - - -
70B VAL* 3.6 9.6 - - + +
71B LEU* 2.9 61.9 + - + +
73B LEU* 4.0 8.1 - - + -
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Residues in contact with ILE 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176A ASN* 3.2 31.6 - - - +
251A LEU* 3.7 24.0 - - + -
258A PHE* 4.1 9.7 - - + -
261A TYR* 3.9 12.1 - - + +
262A VAL* 3.3 28.7 - - + -
266A PHE* 5.6 0.2 - - + -
269A TYR* 3.5 20.4 - - + +
281A ASN* 3.3 4.2 - - + +
282A HIS* 1.3 76.4 - - - +
284A GLU* 1.3 74.2 + - - +
286A GLN* 3.6 2.9 + - - +
287A ALA* 3.2 21.1 + - - +
8B LEU* 4.1 20.9 - - + -
70B VAL* 4.6 7.6 - - + -
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Residues in contact with GLU 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 4.3 0.9 - - + -
226A PHE* 3.9 16.6 - - + -
247A CYS* 3.8 14.5 - - - -
248A MET* 3.6 27.1 - - + -
251A LEU* 4.1 4.8 - - + +
269A TYR* 2.3 35.9 + - - -
273A LYS* 2.9 22.4 + - + +
280A GLY* 4.5 0.4 - - - -
281A ASN* 2.8 35.6 + - - +
283A ILE* 1.3 77.9 - - - +
285A MET* 1.3 60.9 + - - +
287A ALA* 3.3 2.6 + - - +
288A MET* 2.9 39.1 + - + +
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Residues in contact with MET 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.9 28.9 - - + -
229A VAL* 6.0 0.7 - - + -
281A ASN* 3.1 27.2 + - - +
282A HIS* 3.1 9.5 + - - +
284A GLU* 1.3 73.1 - - - +
286A GLN* 1.3 64.9 + - - +
288A MET* 3.4 7.9 + - + -
289A ALA* 3.1 24.3 + - - +
296A VAL* 3.8 19.1 - - + +
298A VAL* 3.8 25.8 - - - -
314A PHE* 3.7 16.1 - - + +
327A VAL* 4.7 0.9 - - - -
335A TYR* 3.1 31.4 - - + +
73B LEU* 3.8 19.5 - - + +
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Residues in contact with GLN 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257A TYR* 5.4 1.5 - - + +
258A PHE* 3.8 15.0 - - + -
282A HIS* 3.0 17.7 + - + +
283A ILE 3.8 4.9 - - - +
285A MET* 1.3 77.8 - - - +
287A ALA* 1.3 61.8 + - - +
289A ALA* 3.5 1.7 + - - +
290A GLU* 2.8 45.5 + - - +
314A PHE* 3.4 30.0 - - - +
315A HIS 3.1 26.4 + - - +
8B LEU* 4.0 35.0 + - + +
9B THR* 4.9 2.5 - - - -
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Residues in contact with ALA 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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247A CYS* 4.3 6.5 - - - +
250A TYR* 3.8 15.6 - - + -
251A LEU* 3.6 40.6 - - + -
258A PHE* 4.0 11.2 - - + -
283A ILE 3.2 8.5 + - - +
284A GLU 3.3 4.7 + - - +
286A GLN* 1.3 81.0 - - - +
288A MET* 1.3 56.3 + - - +
290A GLU* 3.3 3.3 + - - +
291A MET* 2.8 32.7 + - - +
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Residues in contact with MET 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225A LEU* 3.6 31.6 - - + -
226A PHE* 3.9 15.9 - - + -
229A VAL* 3.8 23.8 - - + -
243A VAL* 3.5 29.8 - - - -
247A CYS* 3.8 19.1 - - + -
284A GLU 2.9 24.5 + - - +
285A MET* 4.0 8.3 - - + +
286A GLN 3.3 0.4 - - - -
287A ALA* 1.3 73.9 - - - +
289A ALA* 1.3 65.7 + - - +
291A MET* 4.0 12.1 - - + -
292A TYR* 2.9 37.3 + - + +
296A VAL* 4.5 8.3 - - + -
325A ILE* 4.9 0.6 - - + +
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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
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285A MET 3.1 17.0 + - - +
286A GLN 3.7 6.1 - - - +
287A ALA 3.4 0.2 - - - -
288A MET* 1.3 76.6 - - - +
290A GLU* 1.3 57.2 + - - +
293A ASN* 3.1 7.6 + - - -
294A ARG 3.0 40.7 + - - +
296A VAL* 3.8 9.1 - - + +
314A PHE* 3.4 35.7 - - + +
315A HIS* 3.7 6.7 - - - +
316A GLY 4.4 4.5 + - - -
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Residues in contact with GLU 290 (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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250A TYR* 2.7 40.7 + - - +
254A ASN* 5.2 1.4 + - - -
257A TYR* 4.8 7.0 - - - -
258A PHE* 3.7 19.9 - - - -
286A GLN* 2.8 37.2 + - - +
287A ALA 3.3 4.8 + - - +
288A MET 3.2 0.2 - - - -
289A ALA* 1.3 74.1 - - - +
291A MET* 1.3 67.9 + - - +
293A ASN* 3.1 14.9 + - - +
316A GLY* 3.8 24.4 - - - +
318A HIS* 6.0 2.3 - - - -
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Residues in contact with MET 291 (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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243A VAL 4.7 0.9 - - - +
246A HIS* 3.3 37.7 - - + +
247A CYS* 3.7 12.6 - - + +
250A TYR* 3.8 28.7 - - + -
287A ALA 2.8 18.6 + - - +
288A MET* 3.9 17.5 - - + +
290A GLU* 1.3 79.3 - - - +
292A TYR* 1.3 110.3 + - + +
293A ASN* 3.6 0.7 + - - +
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Residues in contact with TYR 292 (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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229A VAL* 3.8 19.7 - - + -
233A VAL* 4.1 25.6 - - + -
234A TYR* 4.1 15.0 + - - -
243A VAL* 3.5 30.4 - - + +
246A HIS* 4.4 6.7 + - - -
288A MET* 2.9 29.5 + - + +
291A MET* 1.3 108.4 - - + +
293A ASN* 1.3 70.5 + - - +
294A ARG* 3.6 15.4 - - + +
325A ILE* 3.8 27.8 - - + -
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Residues in contact with ASN 293 (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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289A ALA 3.1 9.1 + - - -
290A GLU* 3.1 12.4 + - - +
291A MET 3.3 1.3 - - - +
292A TYR* 1.3 79.2 - - - +
294A ARG* 1.3 61.0 + - - +
295A PRO* 4.8 0.2 - - - -
316A GLY* 5.9 3.6 - - - +
318A HIS* 3.3 40.2 + - + +
319A GLN 3.0 22.8 + - - +
320A ASN* 3.0 19.8 + - - +
321A GLU* 4.3 7.4 + - - +
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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