Contacts of the helix formed by residues 492 - 509 (chain D) in PDB entry 1D7W
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 492 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480D GLY 4.8 4.4 + - - -
483D GLU* 3.7 12.4 + - - -
484D PRO 3.3 16.7 + - - -
485D LEU* 4.2 3.6 - - - +
486D LYS* 4.1 5.2 - - - -
491D VAL* 1.3 74.0 - - - +
493D PRO* 1.4 64.6 - - - +
494D LEU 3.3 2.9 + - - -
495D LEU* 3.5 5.3 + - - +
496D ALA* 2.8 34.7 + - - +
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Residues in contact with PRO 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309D TYR* 4.7 2.4 + - - -
437D ARG* 4.4 7.0 - - - +
442D LEU* 3.8 24.2 - - + +
483D GLU* 3.3 15.5 - - + +
484D PRO* 4.0 11.4 - - + +
486D LYS* 4.1 27.8 - - + -
492D GLY* 1.4 81.9 - - - +
494D LEU* 1.3 57.0 + - - +
496D ALA* 3.7 1.1 - - + +
497D CYS* 2.9 29.8 + - - +
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433D TYR* 3.6 37.9 - - + +
436D TRP* 3.5 29.6 - - + +
437D ARG* 3.7 12.3 - - + +
440D CYS* 3.7 11.7 - - - -
442D LEU* 3.7 7.5 - - + +
476D ILE* 3.8 19.5 - - + -
480D GLY* 4.8 8.5 - - - -
483D GLU* 2.8 26.8 + - - +
493D PRO* 1.3 73.0 - - - +
495D LEU* 1.3 63.5 + - + +
497D CYS* 3.1 6.3 + - - +
498D ILE* 2.9 38.7 + - + +
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Residues in contact with LEU 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D ALA* 3.6 38.4 - - + +
334D TYR* 3.8 24.9 - - + -
476D ILE* 4.9 6.1 - - + +
477D TRP* 5.7 2.2 - - + +
480D GLY* 3.3 45.7 + - - +
481D VAL* 3.8 8.3 - - + +
483D GLU* 4.5 0.2 + - - -
491D VAL* 3.6 25.1 - - + -
492D GLY 3.5 2.9 + - - +
494D LEU* 1.3 78.4 - - - +
496D ALA* 1.3 54.6 + - - +
498D ILE* 4.4 6.7 - - + +
499D ILE* 2.8 41.6 + - + +
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Residues in contact with ALA 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301D LEU* 3.5 17.1 - - + +
305D ALA* 3.8 16.2 - - + -
309D TYR* 3.6 7.0 - - + -
486D LYS* 3.8 24.0 - - + -
491D VAL* 3.6 6.8 - - + +
492D GLY 2.8 20.0 + - - +
493D PRO* 3.7 4.9 - - + +
495D LEU* 1.3 77.2 - - - +
497D CYS* 1.3 53.2 + - - +
500D GLY* 2.8 33.1 + - - -
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Residues in contact with CYS 497 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309D TYR* 3.4 27.1 - - - +
439D PHE* 4.7 2.5 - - - -
440D CYS* 2.0 55.9 - - + -
442D LEU* 5.0 0.7 - - + -
493D PRO 2.9 15.5 + - - +
494D LEU 3.4 4.9 - - - +
496D ALA* 1.3 75.9 - - - +
498D ILE* 1.3 60.3 + - - +
501D THR* 2.8 39.0 + - - -
3E BMA 4.4 12.6 - - - -
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Residues in contact with ILE 498 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.8 14.9 - - + -
327D VAL* 4.0 30.1 - - + -
328D PHE* 4.5 7.4 - - + -
331D ALA* 3.6 27.6 - - + -
436D TRP* 4.4 13.0 - - + -
439D PHE* 5.3 1.1 - - + -
440D CYS* 4.1 11.9 - - - -
476D ILE* 3.9 22.7 - - + -
494D LEU* 2.9 39.2 + - + +
495D LEU* 3.9 4.0 - - + +
497D CYS* 1.3 76.8 - - - +
499D ILE* 1.3 64.1 + - + +
502D GLN* 3.2 22.7 + - - +
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Residues in contact with ILE 499 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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297D LEU* 4.7 3.8 - - + -
300D VAL* 4.6 13.2 - - + -
301D LEU* 4.6 7.0 - - + -
328D PHE* 4.3 10.3 - - + -
331D ALA* 4.2 9.9 - - + +
332D PHE* 3.7 37.0 - - + +
334D TYR* 3.8 22.4 - - + -
491D VAL* 4.4 8.7 - - + -
495D LEU* 2.8 30.6 + - + +
496D ALA 4.3 0.9 - - - +
498D ILE* 1.3 75.1 - - - +
500D GLY* 1.3 60.9 + - - +
502D GLN* 3.3 1.9 + - - +
503D PHE* 3.1 53.6 + - + -
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Residues in contact with GLY 500 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301D LEU* 4.1 16.3 - - - +
309D TYR* 3.7 24.0 - - - +
310D LEU* 4.3 2.7 - - - +
496D ALA 2.8 22.3 + - - -
499D ILE* 1.3 72.8 - - - +
501D THR* 1.3 61.7 + - - +
503D PHE* 3.5 4.3 + - - +
504D ARG* 3.1 25.1 + - - +
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Residues in contact with THR 501 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.5 25.4 - - + -
309D TYR* 3.9 18.0 - - - +
439D PHE* 5.3 0.7 - - + -
497D CYS* 2.8 29.4 + - - -
498D ILE 4.0 0.2 - - - -
500D GLY* 1.3 75.1 - - - +
502D GLN* 1.4 61.3 + - - +
504D ARG* 3.4 6.7 + - - +
505D LYS* 3.2 40.4 + - - +
3E BMA 4.5 9.9 + - - +
5E MAN 4.2 17.0 - - - +
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Residues in contact with GLN 502 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.6 12.3 - - + -
322D PRO 4.5 0.2 + - - -
323D ARG 3.0 24.0 + - - -
324D ILE* 3.4 21.9 - - + +
325D ALA* 2.8 28.8 + - - +
328D PHE* 3.3 48.3 - - + +
498D ILE 3.2 14.4 + - - +
499D ILE 3.6 2.7 - - - +
501D THR* 1.4 75.7 - - - +
503D PHE* 1.3 56.4 + - - +
505D LYS* 3.2 9.6 + - - +
506D LEU* 3.0 35.9 + - + +
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Residues in contact with PHE 503 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B LEU* 3.7 27.6 - - + -
97B LEU* 3.6 31.2 - - + -
171D VAL* 4.8 2.5 - - + -
292D THR* 4.1 6.5 - - + -
293D TYR* 2.6 41.2 + + + +
297D LEU* 3.6 36.6 - - + -
310D LEU* 4.0 7.2 - - + -
328D PHE* 3.8 16.4 - + - -
332D PHE* 3.9 7.2 - + - -
499D ILE* 3.1 49.2 + - + +
500D GLY* 4.2 3.1 - - - +
502D GLN* 1.3 73.1 - - - +
504D ARG* 1.3 66.0 + - - +
506D LEU* 3.2 10.0 + - + -
507D ARG 3.0 8.1 + - - -
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Residues in contact with ARG 504 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308D LYS 5.4 2.6 + - - -
309D TYR 3.3 27.4 - - - +
310D LEU* 3.5 10.0 - - + +
311D PRO* 3.7 27.0 - - - +
314D ARG* 2.7 37.8 - - - +
500D GLY 3.1 11.3 + - - +
501D THR* 3.7 5.8 - - - +
502D GLN 3.3 0.4 - - - -
503D PHE* 1.3 75.6 - - - +
505D LYS* 1.3 57.8 + - - +
507D ARG* 3.2 14.4 + - - +
508D ASP* 2.9 52.5 + - - +
6F FUC 3.1 47.3 + - + -
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Residues in contact with LYS 505 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B TRP* 3.5 38.8 - - + +
320D VAL* 3.8 15.3 - - + +
321D ASP* 3.4 32.7 + - - +
322D PRO* 3.8 8.5 - - + +
323D ARG 5.2 1.3 - - - +
501D THR* 3.2 21.3 + - - +
502D GLN* 3.2 12.7 + - - +
503D PHE 3.1 0.6 - - - -
504D ARG* 1.3 74.9 - - - +
506D LEU* 1.3 60.2 + - - +
509D GLY* 3.0 28.9 + - - -
5E MAN 2.9 34.8 + - - -
6F FUC 4.3 14.1 + - + +
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Residues in contact with LEU 506 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B LEU* 3.5 36.8 - - + -
169D SER* 3.5 23.6 - - - +
170D PHE* 4.5 5.7 - - - +
171D VAL* 4.3 10.6 + - + +
293D TYR* 3.4 14.1 - - - +
322D PRO* 3.3 28.9 - - + +
324D ILE* 3.9 15.7 - - + -
502D GLN* 3.0 25.6 + - + +
503D PHE* 3.2 14.5 + - + +
505D LYS* 1.3 77.4 - - - +
507D ARG* 1.3 56.4 + - - +
510D ASP* 3.2 27.6 - - - +
513D TRP* 4.5 2.4 - - - -
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Residues in contact with ARG 507 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293D TYR* 3.5 20.9 + - + +
306D MET* 5.9 1.8 - - - +
310D LEU* 4.1 18.8 + - - +
311D PRO* 2.8 33.1 + - - +
312D THR* 4.2 2.2 + - - +
313D TYR* 3.5 41.1 + - + +
314D ARG* 5.2 0.4 - - - +
316D TYR* 5.8 0.2 - - - -
503D PHE 3.0 12.1 + - - +
504D ARG* 3.5 19.6 + - - +
505D LYS 3.2 0.2 - - - -
506D LEU* 1.3 78.0 - - - +
508D ASP* 1.3 92.9 + - - +
509D GLY 3.3 0.4 - - - -
510D ASP 3.5 9.5 + - - +
513D TRP* 3.5 56.2 - - + +
515D GLU* 5.4 0.2 - - - -
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Residues in contact with ASP 508 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313D TYR* 3.9 11.8 - - - -
314D ARG* 4.6 3.8 + - - -
315D SER 4.9 5.8 - - - +
316D TYR* 3.4 6.9 - - - -
317D ASN* 3.0 33.1 + - + +
320D VAL* 4.0 20.0 - - + +
504D ARG* 2.9 54.8 + - + +
507D ARG* 1.3 110.4 + - - +
509D GLY* 1.3 57.8 + - - +
510D ASP 3.3 0.9 - - - -
6F FUC 4.2 4.5 - - - +
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Residues in contact with GLY 509 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ASN* 3.8 3.1 - - - +
16B ASN* 5.4 2.8 + - - +
170D PHE* 3.5 5.0 - - - -
316D TYR* 3.7 10.3 + - - -
317D ASN 3.8 4.5 - - - -
320D VAL* 3.5 25.2 - - - +
322D PRO* 3.5 24.5 - - - +
505D LYS 3.0 17.2 + - - -
508D ASP* 1.3 78.8 - - - +
510D ASP* 1.3 57.2 + - - -
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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