Contacts of the helix formed by residues 441 - 459 (chain D) in PDB entry 1Z10
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 441 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135D LEU* 5.7 0.4 - - - -
140D VAL* 6.4 0.2 - - - -
439D CYS* 3.2 10.8 - - - -
440D PHE* 1.3 79.4 - - - +
442D GLU* 1.3 64.9 + - - +
443D GLY 3.4 2.2 - - - -
444D LEU* 3.2 8.6 + - - +
445D ALA* 2.9 22.5 + - - +
500D HEM 3.6 40.6 - - - +
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Residues in contact with GLU 442 (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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432D PHE* 3.4 49.1 - - + +
433D SER 5.2 2.1 - - - +
438D ASN* 4.8 9.0 + - - -
439D CYS* 3.5 17.7 - - - +
440D PHE 3.2 2.2 - - - -
441D GLY* 1.3 78.1 - - - +
443D GLY* 1.3 57.3 + - - +
445D ALA* 3.3 1.0 + - - +
446D ARG* 2.8 67.3 + - - +
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Residues in contact with GLY 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D VAL* 4.8 7.8 - - - +
141D GLY* 5.6 3.8 - - - -
343D PHE* 5.6 0.9 - - - -
440D PHE 4.8 2.8 + - - -
441D GLY 3.4 0.8 - - - -
442D GLU* 1.3 79.2 - - - +
444D LEU* 1.3 63.0 + - - +
446D ARG* 3.4 7.9 + - - +
447D MET* 3.1 28.0 + - - +
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Residues in contact with LEU 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140D VAL* 4.2 25.5 - - + +
141D GLY 5.6 1.3 - - - +
145D ILE* 3.7 30.5 - - + -
149D ILE* 4.1 5.8 - - + -
181D VAL* 4.0 8.5 - - + -
182D ILE* 4.2 9.0 - - + -
185D ILE* 4.2 18.2 - - + -
441D GLY* 3.2 11.7 + - - +
443D GLY* 1.3 74.8 - - - +
445D ALA* 1.3 58.7 + - - +
447D MET* 3.2 6.6 + - + +
448D GLU* 2.8 56.8 + - - +
500D HEM 3.9 30.1 - - + -
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Residues in contact with ALA 445 (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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306D VAL* 4.1 12.1 - - + -
432D PHE* 3.7 25.1 - - + -
441D GLY 2.9 16.7 + - - +
442D GLU 3.7 3.6 - - - +
444D LEU* 1.3 77.2 - - - +
446D ARG* 1.3 53.4 + - - +
448D GLU* 3.2 2.6 + - - +
449D LEU* 2.7 40.7 + - - +
500D HEM 3.9 27.1 - - + +
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Residues in contact with ARG 446 (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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343D PHE* 3.7 14.9 - - + -
357D HIS* 3.2 30.1 + - - -
360D GLN* 5.3 4.2 + - - +
429D PHE* 3.7 27.6 - - - -
432D PHE* 4.4 11.3 - - + -
442D GLU* 2.8 55.0 + - + +
443D GLY* 3.9 7.0 - - - +
445D ALA* 1.3 76.0 - - - +
447D MET* 1.3 57.9 + - - +
449D LEU* 3.9 7.4 - - - +
450D PHE* 3.0 30.5 + - - +
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Residues in contact with MET 447 (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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141D GLY* 4.3 24.9 - - - +
142D LYS 4.9 0.9 - - - +
145D ILE* 4.0 11.0 - - + -
146D GLU* 3.9 33.4 - - + +
149D ILE* 3.6 17.5 - - + -
343D PHE* 3.7 40.5 - - + -
443D GLY 3.1 14.8 + - - +
444D LEU* 3.5 10.1 - - - +
446D ARG* 1.3 75.5 - - - +
448D GLU* 1.3 64.8 + - - +
450D PHE* 4.1 0.3 - - - +
451D LEU* 3.0 36.8 + - + +
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Residues in contact with GLU 448 (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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149D ILE* 3.8 21.3 - - + -
178D VAL* 3.7 24.5 - - - +
181D VAL* 3.3 29.0 - - - +
182D ILE 4.6 1.6 + - - -
302D GLY 4.7 4.7 - - - +
306D VAL* 3.7 18.2 - - + +
444D LEU* 2.8 35.4 + - - +
445D ALA 3.6 4.5 - - - +
447D MET* 1.3 76.3 - - - +
449D LEU* 1.3 58.3 + - - +
452D PHE* 2.9 60.8 + - + +
500D HEM 5.0 0.5 - - - +
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Residues in contact with LEU 449 (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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306D VAL* 4.1 15.0 - - + -
309D THR* 3.7 28.7 - - + -
310D LEU* 4.0 21.5 - - + -
356D ILE* 4.0 17.7 - - + -
360D GLN* 3.5 43.1 - - + +
432D PHE* 5.0 0.7 - - + -
445D ALA 2.7 27.1 + - - +
446D ARG* 3.9 6.7 - - - +
448D GLU* 1.3 73.0 - - - +
450D PHE* 1.3 63.4 + - - +
453D PHE* 3.0 36.3 + - + +
500D HEM 4.5 7.0 - - + -
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Residues in contact with PHE 450 (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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335D ILE* 5.3 0.4 - - + -
341D PRO* 4.9 2.2 - - + -
342D LYS 3.4 22.7 - - - -
343D PHE* 3.8 31.4 - + + -
345D ASP* 3.9 6.5 - - + -
346D ARG* 3.5 35.9 - - + -
349D MET* 4.0 13.2 - - + -
352D MET* 4.0 12.6 - - + -
353D GLU* 4.7 9.0 - - - +
356D ILE* 3.5 19.4 - - + +
446D ARG 3.0 18.6 + - - +
449D LEU* 1.3 75.4 - - - +
451D LEU* 1.3 73.7 + - + +
453D PHE* 4.2 0.2 - - - +
454D THR* 3.0 57.5 + - + +
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Residues in contact with LEU 451 (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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146D GLU* 4.0 19.5 - - + -
149D ILE* 3.8 28.9 - - + -
150D GLN* 4.2 9.4 - - + -
153D ALA* 5.1 2.9 - - + -
341D PRO* 3.5 32.3 - - + +
342D LYS* 3.7 3.6 - - - -
343D PHE* 3.7 20.4 - - - +
447D MET* 3.0 36.8 + - + +
450D PHE* 1.3 85.8 - - + +
452D PHE* 1.3 58.9 + - + +
454D THR* 3.3 1.0 + - - -
455D THR* 2.6 38.7 + - - +
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Residues in contact with PHE 452 (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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149D ILE* 3.7 14.8 - - + -
152D GLU* 4.4 0.9 - - + -
153D ALA* 3.7 31.9 - - + -
156D LEU* 4.7 9.0 - - + -
177D THR* 3.5 31.9 - - + -
178D VAL* 4.2 7.9 - - + -
181D VAL* 3.8 21.8 - - + -
306D VAL* 5.0 0.2 - - + -
310D LEU* 4.1 33.0 - - + -
314D PHE* 5.4 0.9 - - - -
448D GLU* 2.9 56.7 + - + +
451D LEU* 1.3 69.8 - - - +
453D PHE* 1.3 67.1 + - - +
455D THR* 4.3 1.3 - - - -
456D VAL* 3.1 30.9 + - + +
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Residues in contact with PHE 453 (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 THR* 3.9 8.1 - - + -
310D LEU* 3.7 47.1 - - + -
313D GLY* 4.0 7.9 - - - -
314D PHE* 3.8 28.0 - + - -
317D LEU* 4.7 7.6 - - + -
352D MET* 4.4 9.0 - - - -
356D ILE* 3.7 31.0 - - + -
359D ILE* 3.9 28.7 - - + -
449D LEU* 3.0 38.9 + - + +
452D PHE* 1.3 76.4 - - - +
454D THR* 1.3 59.1 + - - +
456D VAL* 4.0 0.5 - - - +
457D MET* 2.9 36.9 + - + +
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Residues in contact with THR 454 (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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331D ILE* 4.1 6.5 - - - +
335D ILE* 4.9 1.1 - - - -
341D PRO* 3.4 25.8 - - - +
349D MET* 4.4 7.0 - - + -
352D MET* 3.5 42.4 - - + -
450D PHE* 3.0 38.9 + - + +
451D LEU* 3.3 5.0 + - - -
453D PHE* 1.3 77.7 - - - +
455D THR* 1.3 59.9 + - - +
458D GLN* 2.8 32.9 + - - +
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Residues in contact with THR 455 (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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153D ALA* 3.9 24.1 - - + +
154D GLY* 5.2 1.1 - - - +
157D ILE* 3.4 24.5 - - + +
340D GLN* 5.4 5.8 - - + +
341D PRO* 3.7 29.7 + - + +
451D LEU* 2.6 26.1 + - - +
452D PHE* 4.3 1.6 - - - -
454D THR* 1.3 74.9 + - - +
456D VAL* 1.3 66.5 + - - +
458D GLN* 3.6 2.4 + - - +
459D ASN* 2.8 35.9 + - - +
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Residues in contact with VAL 456 (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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156D LEU* 3.7 28.9 - - + -
157D ILE* 3.7 14.8 - - + -
160D LEU* 4.1 5.6 - - + -
174D LEU* 5.9 0.4 - - + -
314D PHE* 3.8 19.5 - - + -
452D PHE* 3.1 19.0 + - + +
453D PHE 4.0 0.7 - - - +
455D THR* 1.3 78.6 - - - +
457D MET* 1.3 81.8 + - + +
459D ASN* 3.0 2.8 + - - -
460D PHE* 2.9 31.8 + - + -
491D PHE* 4.0 22.7 - - + -
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Residues in contact with MET 457 (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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314D PHE* 3.3 15.5 - - + -
317D LEU* 4.0 20.2 - - + -
324D GLU* 4.9 5.4 - - - +
327D VAL* 4.2 15.0 - - + -
328D HIS* 3.0 35.0 + - + -
331D ILE* 3.7 18.4 - - + -
352D MET* 4.6 1.8 - - + -
453D PHE* 2.9 24.5 + - + +
456D VAL* 1.3 111.8 - - + +
458D GLN* 1.3 63.7 + - - +
460D PHE 3.1 10.4 - - - +
462D LEU* 3.4 37.7 - - + -
494D ARG* 3.3 1.9 - - - -
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Residues in contact with GLN 458 (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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331D ILE* 3.8 21.0 - - + +
335D ILE* 3.4 9.0 - - - +
336D GLY 2.8 30.7 + - - +
337D LYS* 4.0 20.7 + - + +
339D ARG 3.0 23.6 + - - +
340D GLN* 4.6 1.0 - - - -
341D PRO* 3.4 23.1 - - + +
454D THR 2.8 23.5 + - - +
455D THR* 3.7 2.7 - - - +
457D MET* 1.3 73.8 - - - +
459D ASN* 1.3 73.1 + - - +
494D ARG* 3.1 27.5 + - - +
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Residues in contact with ASN 459 (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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157D ILE* 4.0 9.4 - - + +
161D ARG* 2.7 31.7 + - - +
337D LYS* 5.4 4.8 + - - +
455D THR* 2.8 32.8 + - - +
456D VAL 3.0 2.2 + - - -
458D GLN* 1.3 101.7 + - - +
460D PHE* 1.3 83.3 + - + +
493D PRO* 3.6 2.4 - - - +
494D ARG* 3.1 21.5 + - - +
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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