Contacts of the helix formed by residues 288 - 302 (chain J) in PDB entry 3MQT
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 GLY 288 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103J SER* 3.3 14.4 + - - -
106J ASP* 3.6 3.8 - - - -
107J MET* 5.4 0.7 - - - -
283J TYR 3.4 22.0 + - - -
286J CYS* 3.7 2.6 - - - -
287J GLY* 1.3 79.5 - - - +
289J VAL* 1.3 61.4 + - - -
290J THR 3.2 2.5 - - - -
291J GLU 3.2 1.7 + - - -
292J LEU* 2.8 35.1 + - - +
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Residues in contact with VAL 289 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106J ASP* 2.9 8.4 + - - +
107J MET* 5.3 11.6 - - + +
110J TYR* 3.8 25.4 - - + +
125J MET* 3.8 42.8 - - + -
283J TYR* 4.6 14.1 + - + -
288J GLY* 1.3 70.5 - - - -
290J THR* 1.3 57.8 + - - +
292J LEU* 3.1 7.4 + - - +
293J LEU* 2.7 34.3 + - + +
319J ALA* 4.6 18.8 - - + -
323J PHE* 4.4 12.8 - - + -
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Residues in contact with THR 290 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78J PHE* 3.5 18.1 - - + +
79J ARG* 4.4 12.8 - - + +
82J TYR* 3.8 28.5 - - + -
106J ASP* 2.6 36.0 + - - -
110J TYR* 2.6 25.9 + - - +
289J VAL* 1.3 73.1 - - - +
291J GLU* 1.3 60.8 + - - +
293J LEU* 3.6 8.3 + - - +
294J ARG* 3.5 23.4 + - - +
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Residues in contact with GLU 291 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82J TYR* 3.3 23.9 + - + +
263J THR* 3.3 9.1 - - - -
264J ARG* 2.7 65.7 + - - +
265J PHE* 4.8 1.6 - - - -
286J CYS* 3.6 17.9 - - - +
287J GLY* 3.9 16.7 + - - -
288J GLY 3.2 8.0 + - - +
290J THR* 1.3 76.7 - - - +
292J LEU* 1.3 61.3 + - - +
294J ARG* 2.9 27.8 + - - +
295J ILE* 2.9 21.4 + - + +
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Residues in contact with LEU 292 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281J SER* 3.7 27.4 - - - +
283J TYR* 3.4 49.8 - - + -
286J CYS* 3.7 15.7 - - - -
288J GLY 2.8 22.7 + - - +
289J VAL* 3.5 6.7 - - - +
291J GLU* 1.3 76.3 - - - +
293J LEU* 1.3 57.8 + - - +
295J ILE* 4.2 5.2 - - + -
296J MET* 2.8 30.7 + - - +
306J LEU* 3.6 16.8 - - + +
308J PRO* 4.1 14.1 - - + -
323J PHE* 3.8 15.3 - - + -
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Residues in contact with LEU 293 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110J TYR* 4.1 16.4 - - + +
124J LEU 5.3 0.9 - - - +
125J MET* 4.0 35.0 - - + +
289J VAL* 2.7 26.5 + - + +
290J THR* 3.6 9.6 - - + +
291J GLU 3.2 0.2 - - - -
292J LEU* 1.3 74.6 - - - +
294J ARG* 1.3 61.5 + - + +
296J MET* 3.4 26.1 + - + +
297J ASP* 3.4 26.2 + - - +
323J PHE* 3.7 22.7 - - + -
326J VAL* 4.2 4.5 - - + -
79L ARG* 4.2 14.1 + - - +
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Residues in contact with ARG 294 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79J ARG* 3.6 21.6 - - - +
82J TYR* 6.2 1.3 - - - -
83J ASN* 5.8 1.6 + - - -
264J ARG* 3.3 54.2 - - - +
290J THR* 3.5 13.1 + - - +
291J GLU* 2.9 17.0 + - - +
293J LEU* 1.3 76.1 - - + +
295J ILE* 1.3 65.1 + - - +
297J ASP* 3.3 10.4 + - - +
298J ILE* 3.2 29.8 + - - +
297L ASP* 3.3 49.7 + - - +
300L GLU* 2.8 30.7 + - - +
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Residues in contact with ILE 295 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263J THR 4.2 7.6 - - - +
264J ARG* 3.8 26.2 - - - +
267J ALA* 3.9 23.8 - - + -
271J LEU* 5.5 0.9 - - + -
279J VAL* 4.1 4.0 - - + -
281J SER* 3.5 26.7 - - - +
286J CYS* 4.3 12.6 - - + -
291J GLU* 2.9 18.6 + - + +
292J LEU* 3.2 10.1 + - + +
294J ARG* 1.3 74.9 - - - +
296J MET* 1.3 57.2 + - - +
298J ILE* 3.2 10.4 + - + +
299J CYS* 2.8 42.7 + - - -
306J LEU* 4.0 16.8 - - + -
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Residues in contact with MET 296 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J GLN* 6.0 0.4 - - - +
292J LEU 2.8 17.3 + - - +
293J LEU* 3.5 30.5 - - + +
294J ARG 3.2 0.2 - - - -
295J ILE* 1.3 75.2 - - - +
297J ASP* 1.3 73.4 + - - +
299J CYS* 3.1 5.0 + - - +
300J GLU* 2.9 27.7 + - - +
306J LEU* 3.7 14.5 - - + +
323J PHE* 4.4 2.2 - - + -
326J VAL* 4.3 9.6 - - + +
327J CYS* 3.8 35.7 - - - -
328J HIS* 4.9 11.2 - - + +
329J ILE* 3.6 24.7 - - + +
79L ARG* 3.9 21.5 - - - +
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Residues in contact with ASP 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293J LEU 3.4 10.0 + - - +
294J ARG* 3.3 11.2 + - - +
296J MET* 1.3 81.9 - - - +
298J ILE* 1.3 62.5 + - + +
300J GLU* 3.5 10.4 + - - +
301J HIS* 3.3 19.2 + - - +
79L ARG* 2.8 41.9 + - - -
294L ARG* 3.1 35.9 + - - +
297L ASP* 4.4 11.7 - - + +
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Residues in contact with ILE 298 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264J ARG* 4.1 31.0 - - + +
267J ALA* 6.0 0.9 - - + -
268J GLN* 3.8 46.2 - - + +
271J LEU* 3.6 20.4 - - + -
294J ARG* 3.2 17.7 + - - +
295J ILE* 3.2 10.4 + - + +
297J ASP* 1.3 77.7 - - + +
299J CYS* 1.3 62.8 + - - +
301J HIS* 3.3 7.0 + - + +
302J HIS* 3.2 31.0 + - + +
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Residues in contact with CYS 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271J LEU* 4.0 9.9 - - - -
279J VAL* 3.7 32.5 - - - -
295J ILE* 2.8 33.3 + - - -
296J MET 3.1 7.6 + - - +
298J ILE* 1.3 68.2 - - - +
300J GLU* 1.3 66.5 + - - +
302J HIS 3.0 8.2 + - - +
304J ALA* 3.0 42.1 + - - +
305J GLN 4.2 3.6 - - - -
306J LEU* 4.1 12.3 - - - -
329J ILE* 3.6 9.0 - - + -
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Residues in contact with GLU 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I ASP* 4.4 6.6 - - - +
296J MET* 2.9 13.3 + - - +
297J ASP* 3.6 11.8 - - - +
298J ILE 3.3 0.2 - - - -
299J CYS* 1.3 77.0 - - - +
301J HIS* 1.3 63.0 + - - +
303J ASN* 3.1 14.3 + - - +
304J ALA 4.8 0.7 - - - -
328J HIS* 4.0 27.4 + - - +
329J ILE* 3.9 20.7 - - + +
264L ARG* 2.9 25.4 + - - -
265L PHE* 5.3 1.6 - - - -
294L ARG* 3.1 21.2 + - - +
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Residues in contact with HIS 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240I ASP* 4.1 4.9 - - - +
242I ILE* 3.5 37.8 + - + +
273I LYS* 4.4 15.5 + - - -
297J ASP 3.3 10.1 + - - +
298J ILE* 3.3 11.3 + - - +
299J CYS 3.3 0.4 - - - -
300J GLU* 1.3 78.7 - - - +
302J HIS* 1.3 79.5 + + - +
303J ASN 3.3 3.5 + - - -
265L PHE* 6.1 3.2 - - - -
268L GLN* 3.2 38.9 + - + +
272L GLU* 4.5 6.3 + - - -
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Residues in contact with HIS 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242I ILE* 3.6 26.0 - - + +
246I LYS* 3.1 28.2 + - - +
268J GLN* 5.1 1.6 - - + -
271J LEU* 3.9 43.6 - - + +
272J GLU* 3.0 30.1 + - - -
298J ILE* 3.2 29.5 + - + +
299J CYS 3.0 8.8 + - - +
301J HIS* 1.3 93.1 - + - +
303J ASN* 1.3 68.4 + - - +
304J ALA* 3.1 4.9 + - + +
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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