Contacts of the helix formed by residues 371 - 387 (chain N) in PDB entry 3L73
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 371 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N GLN* 5.3 2.9 - - - -
369N LEU 3.5 2.8 + - - -
370N ASP* 1.3 75.7 + - - +
372N THR* 1.3 64.5 + - - -
373N THR 3.5 0.9 - - - -
374N PRO* 3.5 6.3 - - - -
375N VAL* 2.8 28.4 + - - +
373O GLU* 4.0 26.6 + - - -
374O THR* 4.9 0.4 - - - -
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Residues in contact with THR 372 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32N GLN* 3.9 18.6 - - - +
34N THR 4.2 3.1 - - - +
35N CYS* 3.8 8.9 - - - -
36N THR* 2.7 24.6 + - - -
100N LYS* 3.6 0.3 + - - -
200N ALA* 3.6 30.8 - - + +
201N GLY* 3.7 16.4 - - - +
371N GLY* 1.3 71.2 - - - -
373N THR* 1.3 65.7 + - - +
375N VAL* 3.2 1.3 + - - -
376N CYS* 2.9 24.1 + - - +
373O GLU* 2.9 30.4 + - - -
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Residues in contact with THR 373 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N THR* 3.2 13.7 + - + -
40N TRP* 5.0 1.7 - - + -
98N TYR* 3.4 41.7 - - + +
100N LYS* 3.0 34.4 + - + +
372N THR* 1.3 78.9 + - - +
374N PRO* 1.3 67.3 - - + +
376N CYS* 2.9 4.9 + - + +
377N GLU* 2.8 30.4 + - + +
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Residues in contact with PRO 374 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100N LYS* 5.9 0.2 - - - +
367N ALA 5.5 1.1 - - - +
368N GLN* 3.0 31.3 - - - +
370N ASP 3.2 35.7 - - - +
371N GLY* 3.5 8.7 - - - +
373N THR* 1.3 95.5 - - + +
375N VAL* 1.3 56.7 + - - -
377N GLU* 3.9 9.0 - - + +
378N THR* 3.1 18.9 + - - -
373O GLU* 5.6 0.4 - - - +
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Residues in contact with VAL 375 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28N GLU* 4.0 27.4 - - + +
200N ALA* 4.2 15.9 - - + -
369N LEU* 3.6 34.5 - - + +
371N GLY 2.8 25.5 + - - +
372N THR* 3.2 4.8 + - - +
373N THR 3.2 1.0 - - - -
374N PRO* 1.3 76.3 - - - +
376N CYS* 1.3 64.0 + - - +
378N THR* 3.5 3.0 - - - -
379N ILE* 3.2 29.1 + - + +
389N ARG* 4.6 11.4 - - - +
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Residues in contact with CYS 376 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N THR* 3.7 20.2 - - + -
37N VAL* 4.2 4.0 - - - -
40N TRP* 3.2 39.4 - - + -
198N ALA* 3.3 28.9 - - - +
199N ALA* 3.9 1.3 - - - -
200N ALA* 4.2 8.9 - - + +
372N THR 2.9 16.7 + - - +
373N THR 2.9 4.9 + - - +
375N VAL* 1.3 77.8 - - - +
377N GLU* 1.3 60.2 + - - +
378N THR 3.1 0.4 - - - -
379N ILE* 3.3 6.1 + - - +
380N GLY* 2.8 27.2 + - - -
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Residues in contact with GLU 377 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N TRP* 2.9 27.0 + - + -
89N TYR* 2.4 45.9 + - - -
94N GLN* 3.4 0.2 + - - -
98N TYR* 5.0 3.6 - - - -
373N THR* 2.8 18.1 + - + +
374N PRO* 3.9 10.3 - - + +
376N CYS* 1.3 76.4 - - - +
378N THR* 1.3 62.2 + - - +
380N GLY 3.7 0.2 + - - -
381N SER* 3.0 43.6 + - - +
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Residues in contact with THR 378 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368N GLN* 3.9 7.8 + - - +
369N LEU* 3.2 20.3 - - + +
374N PRO 3.1 13.8 + - - -
375N VAL 3.5 9.4 - - - -
376N CYS 3.1 0.4 - - - -
377N GLU* 1.3 77.8 - - - +
379N ILE* 1.3 56.5 + - - +
381N SER* 3.1 4.1 + - - -
382N HIS* 2.6 65.9 + - + +
389N ARG* 3.7 24.5 - - - +
390N ILE 5.4 0.2 - - - +
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Residues in contact with ILE 379 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N THR* 3.9 17.5 - - + -
26N ALA* 3.8 29.2 - - + -
27N SER* 4.1 3.1 - - - -
28N GLU* 3.9 26.2 - - + +
198N ALA* 3.8 13.7 - - + -
199N ALA 4.2 5.8 - - - +
200N ALA* 5.0 0.2 - - + -
375N VAL* 3.2 17.3 + - + +
376N CYS* 3.3 7.6 + - - +
378N THR* 1.3 79.4 - - - +
380N GLY* 1.3 65.8 + - - +
381N SER 3.1 1.0 + - - -
382N HIS* 4.5 4.5 - - - -
383N LEU* 3.2 27.4 + - + +
389N ARG* 3.2 31.4 - - + +
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Residues in contact with GLY 380 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N TRP* 3.5 42.2 - - - +
196N VAL* 4.5 7.9 - - - +
198N ALA* 3.8 5.4 - - - +
376N CYS 2.8 14.8 + - - -
379N ILE* 1.3 74.7 - - - +
381N SER* 1.3 57.2 + - - +
383N LEU* 4.2 2.3 - - - +
384N LEU* 3.2 25.5 + - - +
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Residues in contact with SER 381 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N TRP* 4.2 0.2 - - - -
94N GLN* 2.9 28.0 + - - +
377N GLU* 3.0 24.9 + - - +
378N THR* 3.6 3.6 - - - -
380N GLY* 1.3 74.2 - - - +
382N HIS* 1.3 69.2 + - - +
384N LEU* 3.1 5.1 + - - -
385N ASN* 2.7 41.1 + - - +
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Residues in contact with HIS 382 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378N THR* 2.6 46.3 + - + +
379N ILE* 3.2 3.6 + - - +
381N SER* 1.3 72.3 - - - +
383N LEU* 1.3 57.1 + - - +
386N TYR* 2.5 52.3 + + - -
387N GLY 3.1 2.8 + - - -
388N ARG 2.9 15.5 - - - +
389N ARG* 3.4 15.8 - - - -
390N ILE* 2.8 60.4 + - + +
395N TRP* 3.9 15.7 + - - -
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Residues in contact with LEU 383 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14N THR* 6.4 0.2 - - + -
16N VAL* 3.9 31.6 - - + -
24N ARG* 3.8 18.7 + - + +
26N ALA* 3.5 25.6 - - + -
196N VAL* 3.2 39.0 - - + -
379N ILE* 3.2 15.7 + - + +
382N HIS* 1.3 77.2 - - + +
384N LEU* 1.3 60.8 - - - +
387N GLY* 2.7 32.0 + - - +
388N ARG* 3.3 30.3 + - - +
389N ARG* 4.2 2.9 - - + +
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Residues in contact with LEU 384 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24N ARG* 4.4 17.6 + - - +
40N TRP* 3.6 24.0 - - + +
41N ILE 3.5 28.9 - - - +
42N GLY* 3.6 20.6 - - - +
93N GLU 5.9 0.7 - - - +
94N GLN* 4.3 18.2 - - + +
194N ARG* 4.0 11.4 - - - +
196N VAL* 4.5 7.3 - - + +
380N GLY 3.2 12.5 + - - +
381N SER* 3.1 5.8 + - - +
383N LEU* 1.3 80.7 - - - +
385N ASN* 1.3 61.6 + - - +
387N GLY 5.0 0.2 + - - -
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Residues in contact with ASN 385 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93N GLU* 5.3 3.3 - - - +
94N GLN* 3.8 20.9 + - - +
262N TRP* 3.5 62.9 + - + +
263N ALA* 5.4 3.8 + - - +
315N SER* 5.7 1.2 - - - -
381N SER* 2.7 32.5 + - - +
384N LEU* 1.3 80.1 - - - +
386N TYR* 1.3 71.0 + - + +
387N GLY 3.4 1.1 - - - -
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Residues in contact with TYR 386 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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262N TRP* 3.3 60.3 + + + -
263N ALA* 4.9 4.9 - - - -
267N ASN* 6.0 1.6 - - - +
381N SER 5.9 0.2 - - - -
382N HIS* 2.5 44.7 + + - +
385N ASN* 1.3 79.8 - - + +
387N GLY* 1.3 60.4 + - - +
388N ARG* 3.4 18.8 + - + +
390N ILE* 3.5 30.1 - - + -
395N TRP* 3.7 30.3 - + - -
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Residues in contact with GLY 387 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ARG* 4.8 8.5 - - - -
383N LEU* 2.7 24.9 + - - +
385N ASN 3.4 1.6 - - - -
386N TYR* 1.3 78.3 - - - +
388N ARG* 1.3 64.5 + - - +
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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
------------------------------------------------------------
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