Contacts of the helix formed by residues 317 - 335 (chain P) 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 P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0P NAD 4.3 9.7 + - - +
12P ARG* 2.8 58.2 + - + +
13P ILE* 4.1 6.4 - - + +
16P LEU* 3.6 12.3 - - + -
50P MET* 4.6 1.8 - - - +
51P GLN* 2.9 15.5 + - - +
238P ALA 4.3 0.3 - - - +
239P THR* 3.3 22.4 + - - +
315P ASP* 2.8 7.3 + - - +
316P ASN* 1.3 85.7 - - - +
318P MET* 1.3 62.7 + - - +
320P TYR* 3.4 2.3 + - - +
321P THR* 2.7 33.7 + - - -
187Q GLN* 4.0 13.7 + - - +
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Residues in contact with MET 318 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16P LEU* 4.3 26.5 - - + +
19P ARG* 5.3 9.2 - - + +
20P ARG* 4.5 18.8 - - + -
51P GLN* 4.0 17.7 - - + +
285P GLY* 3.5 20.6 - - - +
286P MET 3.4 16.2 - - - +
287P THR* 4.4 4.9 - - + -
315P ASP* 3.2 20.7 - - - +
317P GLU* 1.3 77.5 - - - +
319P SER* 1.3 59.9 + - - +
321P THR* 4.1 17.9 - - - -
322P ALA* 2.8 28.9 + - - +
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Residues in contact with SER 319 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154P ASN* 5.9 0.2 - - - -
286P MET* 3.3 19.9 + - - +
287P THR 4.7 1.1 - - - -
288P TYR 2.6 26.5 + - - -
289P GLY* 3.9 15.0 - - - -
314P TYR* 4.0 4.3 - - - -
315P ASP* 2.8 39.7 + - - +
318P MET* 1.3 69.6 - - - +
320P TYR* 1.3 64.8 + - - +
322P ALA* 3.5 2.1 + - - +
323P GLN* 3.1 27.2 + - - +
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Residues in contact with TYR 320 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0P NAD 3.3 17.9 - + - -
13P ILE* 4.3 11.0 - - + -
120P SER* 2.9 43.7 - - - -
121P ALA 3.2 0.5 + - - -
148P GLY 3.2 22.6 + - - -
149P ALA 2.6 30.1 + - - -
150P SER 3.5 9.9 - - - -
151P GLY* 3.4 23.8 - - - -
154P ASN* 3.6 9.6 - - - -
314P TYR* 6.0 0.2 - - - -
315P ASP 3.5 1.6 + - - -
316P ASN 3.3 20.6 - - - +
317P GLU 3.4 1.2 + - - +
318P MET 3.3 0.2 - - - -
319P SER* 1.3 79.2 - - - +
321P THR* 1.3 60.7 + - - +
323P GLN* 3.1 8.3 + - - +
324P LEU* 2.8 42.1 + - + +
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Residues in contact with THR 321 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 3.9 18.5 - - - +
16P LEU* 3.5 19.5 - - + +
17P ALA* 3.4 40.6 - - + +
20P ARG* 4.2 8.5 - - + -
317P GLU 2.7 26.1 + - - -
318P MET* 3.7 11.7 - - - -
320P TYR* 1.3 76.5 - - - +
322P ALA* 1.3 61.5 + - - +
324P LEU* 3.3 6.8 + - + +
325P VAL* 2.9 29.3 + - - +
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Residues in contact with ALA 322 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ARG* 3.9 30.3 + - - +
287P THR* 3.4 35.2 - - + +
318P MET* 2.8 20.0 + - - +
319P SER 4.0 0.7 - - - +
321P THR* 1.3 73.6 - - - +
323P GLN* 1.3 61.5 + - - +
325P VAL* 3.4 1.6 + - - +
326P ARG* 3.1 34.8 + - - +
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Residues in contact with GLN 323 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131P VAL* 3.7 5.3 - - - +
132P PHE* 2.8 35.7 + - + +
148P GLY 5.9 0.4 - - - +
154P ASN* 3.0 38.1 + - + +
270P SER* 2.6 29.9 + - - -
289P GLY* 3.6 18.1 - - - -
319P SER 3.1 18.6 + - - +
320P TYR* 3.5 7.6 - - + +
322P ALA* 1.3 73.1 - - - +
324P LEU* 1.3 59.2 + - - +
326P ARG* 3.0 22.6 + - - +
327P THR* 2.9 32.6 + - - -
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Residues in contact with LEU 324 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13P ILE* 3.9 17.7 - - + -
17P ALA* 4.9 3.8 - - + -
94P LEU* 3.8 30.7 - - + -
96P CYS* 4.7 0.7 - - - -
118P LEU* 3.6 23.4 - - + +
119P ILE 4.6 0.2 - - - -
120P SER* 3.7 28.5 - - - -
148P GLY* 3.9 17.0 + - - +
320P TYR* 2.8 41.4 + - + +
321P THR* 3.5 9.6 - - - +
323P GLN* 1.3 71.7 - - - +
325P VAL* 1.3 59.2 + - - +
327P THR* 3.4 3.3 + - - -
328P LEU* 2.7 29.3 + - - +
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Residues in contact with VAL 325 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17P ALA* 4.2 28.9 - - + +
20P ARG* 4.0 22.0 - - + +
21P ILE* 4.1 22.7 - - + -
24P VAL* 4.2 20.2 - - + -
27P LEU* 4.1 11.7 - - + -
94P LEU* 5.2 1.3 - - + -
321P THR 2.9 20.5 + - - +
322P ALA 4.0 3.1 - - - +
323P GLN 3.2 0.2 - - - -
324P LEU* 1.3 75.0 - - + +
326P ARG* 1.3 61.6 + - + +
328P LEU* 3.4 7.8 - - + +
329P ALA* 3.0 27.0 + - - +
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Residues in contact with ARG 326 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P ARG* 4.2 15.3 - - - +
132P PHE* 3.6 40.5 - - + -
269P GLU* 3.3 38.2 + - - +
270P SER* 4.2 2.4 - - - +
287P THR* 2.9 43.4 + - - -
289P GLY 4.3 0.2 - - - +
322P ALA* 3.1 30.2 + - - +
323P GLN* 3.0 27.4 + - - +
325P VAL* 1.3 74.6 - - + +
327P THR* 1.3 65.8 + - - +
329P ALA* 3.3 7.5 + - - +
330P TYR* 3.0 23.2 + - - +
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Residues in contact with THR 327 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P LEU* 4.2 22.7 - - + -
130P ILE* 3.6 38.0 + - + +
132P PHE* 3.5 25.0 + - + +
139P LEU* 4.3 12.3 - - + +
146P VAL* 4.8 1.6 - - + -
148P GLY* 5.5 2.0 - - - -
323P GLN 2.9 17.5 + - - -
324P LEU* 3.7 5.6 - - - -
326P ARG* 1.3 76.5 - - - +
328P LEU* 1.3 56.8 + - - +
330P TYR* 3.8 1.7 - - - +
331P LEU* 2.8 34.9 + - + +
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Residues in contact with LEU 328 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5P VAL* 4.2 20.4 - - + -
21P ILE* 3.9 28.9 - - + -
27P LEU* 4.1 20.0 - - + -
92P VAL* 3.5 42.8 - - + -
94P LEU* 4.2 14.4 - - + -
118P LEU* 3.7 14.5 - - + +
324P LEU 2.7 21.5 + - - +
325P VAL* 3.4 8.1 - - - +
327P THR* 1.3 73.2 - - - +
329P ALA* 1.3 58.6 + - - +
331P LEU* 3.5 4.3 - - + +
332P ALA* 2.8 32.3 + - + +
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Residues in contact with ALA 329 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P VAL* 4.7 10.5 - - + -
27P LEU* 4.1 24.9 - - + -
325P VAL 3.0 16.7 + - - +
326P ARG* 3.3 6.7 + - - +
328P LEU* 1.3 75.6 - - - +
330P TYR* 1.3 61.7 + - - +
332P ALA* 3.3 2.4 + - - +
333P GLU* 3.0 33.8 + - - +
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Residues in contact with TYR 330 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132P PHE* 3.7 14.4 - + + -
136P HIS* 3.3 52.0 - + + -
137P GLN* 4.1 18.6 + - + +
139P LEU* 4.2 16.2 + - + -
326P ARG 3.0 16.8 + - - +
327P THR* 3.8 3.6 - - - +
329P ALA* 1.3 74.6 - - - +
331P LEU* 1.3 64.9 + - - +
333P GLU* 3.3 12.8 + - + +
334P LEU* 3.3 52.5 + - + +
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Residues in contact with LEU 331 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P VAL* 4.7 12.3 - - + -
116P LYS* 4.1 30.2 - - + +
117P VAL 4.8 3.4 - - - +
118P LEU* 4.2 28.0 - - + -
139P LEU* 4.4 14.6 - - + -
141P GLY* 5.5 0.4 - - - -
143P GLU* 4.2 17.0 - - - +
144P THR 6.5 0.4 - - - -
146P VAL* 4.1 32.3 - - + -
327P THR* 2.8 23.3 + - + +
328P LEU* 3.5 4.7 - - + +
330P TYR* 1.3 77.1 - - - +
332P ALA* 1.3 63.0 + - - +
334P LEU* 3.4 19.7 + - + +
335P SER* 3.9 6.4 + - - -
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Residues in contact with ALA 332 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P VAL* 3.7 43.3 - - + +
27P LEU* 4.9 1.8 - - + -
91P ASP* 5.7 0.7 - - + -
92P VAL* 4.2 14.8 - - + -
116P LYS* 5.3 2.0 - - - +
328P LEU* 2.8 20.5 + - + +
329P ALA* 3.9 4.5 - - - +
331P LEU* 1.3 74.6 - - - +
333P GLU* 1.3 62.5 + - - +
334P LEU 3.3 0.5 + - - -
335P SER* 3.4 21.2 + - - +
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Residues in contact with GLU 333 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3P VAL* 5.9 1.3 - - - -
329P ALA* 3.0 24.9 + - - +
330P TYR* 3.6 12.4 - - + +
331P LEU 3.2 0.2 - - - -
332P ALA* 1.3 77.4 - - - +
334P LEU* 1.3 61.5 + - + +
335P SER 3.5 5.6 + - - +
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Residues in contact with LEU 334 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139P LEU* 3.6 28.9 - - + +
140P ASP* 3.6 12.9 - - - +
141P GLY* 3.4 36.3 - - - +
143P GLU* 4.7 0.7 - - - +
330P TYR* 3.3 39.3 + - + +
331P LEU* 3.7 11.2 - - + +
332P ALA 3.2 1.2 - - - -
333P GLU* 1.3 77.6 - - - +
335P SER* 1.3 64.8 + - - +
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Residues in contact with SER 335 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116P LYS* 3.1 31.8 - - - -
141P GLY* 5.0 6.0 - - - -
331P LEU 3.9 0.5 + - - -
332P ALA* 3.4 14.7 + - - +
333P GLU 3.5 6.4 - - - +
334P LEU* 1.3 80.6 - - - +
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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