Contacts of the helix formed by residues 317 - 335 (chain R) in PDB entry 3K9Q
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 GLU 317 (chain R).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187O GLN* 4.2 11.6 + - - +
0R NAD 4.3 11.5 + - - +
12R ARG* 2.8 49.3 + - + +
13R ILE* 4.1 6.4 - - + +
16R LEU* 3.6 12.8 - - + -
50R MET* 4.6 2.6 - - - +
51R GLN* 2.9 20.3 + - - +
238R ALA 4.4 1.6 - - - +
239R THR* 3.3 23.4 + - - +
315R ASP* 2.8 7.5 + - - +
316R ASN* 1.3 87.0 - - - +
318R MET* 1.3 62.1 + - - +
320R TYR* 3.3 2.4 + - - +
321R THR* 2.7 34.5 + - - -
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Residues in contact with MET 318 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16R LEU* 4.3 28.3 - - + +
19R ARG* 5.2 10.1 - - + +
20R ARG* 4.4 19.3 - - + -
51R GLN* 4.2 15.5 - - + +
285R GLY* 3.6 19.3 - - - +
286R MET 3.3 17.5 - - - +
287R THR* 4.3 6.5 - - + -
315R ASP* 3.2 20.3 - - - +
317R GLU* 1.3 80.8 - - - +
319R SER* 1.3 57.4 + - - +
321R THR* 4.1 17.9 - - - -
322R ALA* 2.8 29.5 + - - +
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Residues in contact with SER 319 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154R ASN* 5.9 0.4 - - - -
286R MET* 3.5 17.8 + - - +
288R TYR 2.7 27.2 + - - -
289R GLY* 3.8 16.6 - - - -
314R TYR* 4.0 4.0 - - - -
315R ASP* 2.7 43.7 + - - +
318R MET* 1.3 69.3 - - - +
320R TYR* 1.3 61.9 - - - -
322R ALA* 3.9 2.8 - - - +
323R GLN* 3.1 27.2 + - - +
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Residues in contact with TYR 320 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0R NAD 3.4 17.7 - + - -
13R ILE* 4.2 10.8 - - + -
120R SER* 2.9 43.6 - - - -
121R ALA 3.2 0.7 + - - -
148R GLY 3.2 23.2 + - - -
149R ALA 2.6 29.4 + - - -
150R SER 3.3 25.1 - - - -
151R GLY* 3.7 9.4 - - - -
154R ASN* 3.5 10.5 - - - -
314R TYR* 6.0 0.2 - - - -
315R ASP 3.5 1.6 + - - -
316R ASN* 3.3 19.9 - - - +
317R GLU 3.3 0.6 + - - -
318R MET 3.3 0.4 - - - -
319R SER* 1.3 78.4 - - - +
321R THR* 1.3 55.2 + - - +
323R GLN* 3.1 7.1 + - + +
324R LEU* 2.7 51.5 + - + +
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Residues in contact with THR 321 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ILE* 3.7 20.0 - - + +
16R LEU* 3.4 43.2 - - + +
17R ALA* 3.4 15.5 - - + +
20R ARG* 4.3 8.1 - - + -
317R GLU 2.7 25.9 + - - -
318R MET* 3.7 10.5 - - - -
320R TYR* 1.3 77.6 - - - +
322R ALA* 1.3 58.7 + - - +
324R LEU* 3.1 8.7 + - - +
325R VAL* 2.9 29.2 + - + +
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Residues in contact with ALA 322 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R ARG* 3.8 28.7 + - - +
287R THR* 3.4 32.3 - - + +
318R MET* 2.8 21.1 + - - +
319R SER 3.9 1.3 - - - +
321R THR* 1.3 73.5 - - - +
323R GLN* 1.3 62.4 + - - +
325R VAL* 3.4 1.6 + - - +
326R ARG* 3.1 36.6 + - - +
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Residues in contact with GLN 323 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131R VAL* 3.7 5.9 - - - +
132R PHE* 2.8 36.1 + - + +
148R GLY 6.0 0.4 - - - +
154R ASN* 3.1 37.5 + - + +
270R SER* 2.7 29.5 + - - -
289R GLY* 3.6 17.4 - - - -
319R SER 3.1 17.7 + - - +
320R TYR* 3.1 9.4 + - + +
322R ALA* 1.3 75.0 - - - +
324R LEU* 1.3 62.7 + - - +
326R ARG* 3.0 23.8 + - - +
327R THR* 3.0 28.1 + - - -
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Residues in contact with LEU 324 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13R ILE* 3.8 17.0 - - + -
17R ALA* 5.0 2.2 - - + -
94R LEU* 3.8 30.3 - - + -
96R CYS* 4.6 0.4 - - - -
118R LEU* 3.6 22.1 - - + +
120R SER* 3.6 30.5 - - - -
148R GLY* 4.0 16.2 - - - -
320R TYR* 2.7 42.9 + - + +
321R THR* 3.1 10.5 + - - +
323R GLN* 1.3 73.0 - - - +
325R VAL* 1.3 58.4 + - + +
327R THR* 3.5 3.0 + - - -
328R LEU* 2.8 28.8 + - - +
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Residues in contact with VAL 325 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17R ALA* 4.2 21.1 - - + +
20R ARG* 4.2 19.7 - - + +
21R ILE* 4.0 31.4 - - + -
24R VAL* 4.2 19.5 - - + -
27R LEU* 4.1 13.5 - - + -
94R LEU* 5.2 1.3 - - + -
321R THR 2.9 18.9 + - - +
322R ALA 4.1 3.6 - - - +
323R GLN 3.2 0.2 - - - -
324R LEU* 1.3 75.7 - - + +
326R ARG* 1.3 66.5 + - + +
328R LEU* 3.6 6.9 - - + +
329R ALA* 3.0 22.5 + - - +
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Residues in contact with ARG 326 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20R ARG* 4.0 14.9 - - - +
132R PHE* 3.6 40.7 - - + -
269R GLU* 3.5 36.3 + - - +
270R SER* 4.0 2.4 + - - -
287R THR* 2.9 42.8 + - - -
289R GLY 4.3 1.2 - - - +
322R ALA* 3.1 25.4 + - - +
323R GLN* 3.0 30.9 + - - +
325R VAL* 1.3 79.2 - - + +
327R THR* 1.3 62.9 + - - +
329R ALA* 3.2 5.7 + - - +
330R TYR* 3.0 22.0 + - - +
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Residues in contact with THR 327 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118R LEU* 4.2 22.7 - - + -
130R ILE* 3.8 35.3 + - + +
132R PHE* 3.4 26.8 + - - +
136R HIS* 5.5 0.4 - - + -
139R LEU* 4.5 11.4 - - + -
146R VAL* 5.0 1.1 - - + -
148R GLY* 5.3 2.9 - - - -
323R GLN 3.0 16.0 + - - -
324R LEU* 3.7 6.7 - - - -
326R ARG* 1.3 74.6 - - - +
328R LEU* 1.3 52.7 + - - +
330R TYR* 3.2 3.3 + - - +
331R LEU* 2.7 39.5 + - + +
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Residues in contact with LEU 328 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5R VAL* 4.1 18.2 - - + -
21R ILE* 3.9 27.1 - - + -
27R LEU* 4.3 16.4 - - + -
92R VAL* 3.5 43.3 - - + -
94R LEU* 4.1 19.5 - - + -
118R LEU* 3.7 15.4 - - + +
324R LEU 2.8 20.7 + - - +
325R VAL* 3.6 8.3 - - - +
326R ARG 3.3 0.2 - - - -
327R THR* 1.3 71.4 - - - +
329R ALA* 1.3 54.7 + - - +
331R LEU* 3.4 4.2 - - + +
332R ALA* 2.8 37.7 + - + +
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Residues in contact with ALA 329 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24R VAL* 4.8 9.0 - - + -
27R LEU* 4.0 26.2 - - + -
325R VAL 3.0 17.5 + - - +
326R ARG* 3.5 5.8 - - - +
328R LEU* 1.3 78.0 - - - +
330R TYR* 1.3 62.1 + - - +
332R ALA* 3.4 2.1 + - - +
333R GLU* 3.0 32.0 + - - +
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Residues in contact with TYR 330 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132R PHE* 3.8 14.8 - + + -
136R HIS* 3.2 51.6 - + + -
137R GLN* 4.0 20.0 + - + +
139R LEU* 4.2 15.6 + - + -
326R ARG 3.0 15.2 + - - +
327R THR* 3.7 3.8 - - - +
329R ALA* 1.3 75.1 - - - +
331R LEU* 1.3 63.5 + - - +
333R GLU* 3.3 22.1 + - + +
334R LEU* 3.4 48.0 + - + +
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Residues in contact with LEU 331 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92R VAL* 4.6 11.0 - - + -
116R LYS* 4.0 30.8 - - + +
117R VAL 4.8 3.8 - - - +
118R LEU* 4.3 27.6 - - + -
139R LEU* 4.3 20.2 - - + -
141R GLY* 5.7 0.4 - - - -
143R GLU* 4.4 9.4 - - + +
146R VAL* 4.1 33.7 - - + -
327R THR* 2.7 22.6 + - + +
328R LEU 3.4 4.0 - - - +
330R TYR* 1.3 77.0 - - - +
332R ALA* 1.3 61.9 + - - +
334R LEU* 3.4 20.9 + - + +
335R SER* 3.9 5.9 + - - -
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Residues in contact with ALA 332 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R VAL* 3.7 42.2 - - + +
27R LEU* 4.8 1.8 - - + -
91R ASP* 5.8 0.7 - - + -
92R VAL* 4.2 15.3 - - + -
116R LYS* 5.1 2.0 - - - +
328R LEU* 2.8 20.0 + - + +
329R ALA* 3.9 5.6 - - - +
331R LEU* 1.3 74.3 - - - +
333R GLU* 1.3 61.5 + - - +
334R LEU 3.3 1.0 + - - -
335R SER* 3.3 20.5 + - - +
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Residues in contact with GLU 333 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3R VAL* 5.9 1.6 - - - -
329R ALA* 3.0 24.8 + - - +
330R TYR* 3.7 12.8 - - + +
331R LEU 3.3 0.2 - - - -
332R ALA* 1.3 76.5 - - - +
334R LEU* 1.3 62.0 + - + +
335R SER 3.5 4.9 - - - +
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Residues in contact with LEU 334 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139R LEU* 3.7 32.1 - - + +
140R ASP* 4.6 7.4 - - - +
141R GLY* 3.4 37.3 - - - +
143R GLU* 4.8 0.7 - - - +
330R TYR* 3.4 37.7 - - + +
331R LEU* 3.4 13.0 + - + +
332R ALA 3.2 1.0 - - - -
333R GLU* 1.3 76.9 - - + +
335R SER* 1.3 65.5 + - - +
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Residues in contact with SER 335 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116R LYS* 3.1 31.3 - - - -
141R GLY* 5.0 7.1 - - - -
331R LEU 3.9 0.2 + - - -
332R ALA* 3.3 16.5 + - - +
333R GLU 3.5 5.8 - - - +
334R LEU* 1.3 82.4 - - - +
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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
------------------------------------------------------------
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