Contacts of the helix formed by residues 441 - 459 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 5.6 0.4 - - - -
439B CYS* 3.2 8.9 - - - -
440B PHE* 1.3 80.1 - - - +
442B GLU* 1.3 64.5 + - - +
443B GLY 3.3 2.2 - - - -
444B LEU* 3.1 9.6 + - - +
445B ALA* 2.9 22.0 + - - +
500B HEM 3.6 41.1 - - - +
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Residues in contact with GLU 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429B PHE* 5.5 1.2 - - - -
432B PHE* 3.4 53.8 - - + +
433B SER 5.2 1.9 - - - +
438B ASN* 4.7 8.5 + - - -
439B CYS* 3.4 19.0 - - - +
440B PHE 3.2 2.0 - - - -
441B GLY* 1.3 77.9 - - - +
443B GLY* 1.3 58.9 + - - +
445B ALA* 3.7 0.7 - - - +
446B ARG* 2.9 54.5 + - + +
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Residues in contact with GLY 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140B VAL* 5.1 5.2 - - - -
141B GLY* 6.0 3.6 - - - -
343B PHE* 5.1 2.3 - - - -
440B PHE 4.8 2.8 + - - -
441B GLY 3.3 0.6 - - - -
442B GLU* 1.3 80.3 - - - +
444B LEU* 1.3 64.3 + - - +
446B ARG* 3.4 5.1 + - - +
447B MET* 3.1 25.3 + - - +
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Residues in contact with LEU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135B LEU* 5.8 0.4 - - + -
140B VAL* 4.4 25.2 - - + +
141B GLY 6.0 0.2 - - - +
145B ILE* 4.0 23.8 - - + -
149B ILE* 4.1 8.5 - - + -
181B VAL* 3.9 15.9 - - + -
182B ILE* 4.2 9.6 - - + -
185B ILE* 4.2 19.3 - - + -
440B PHE 5.5 0.4 + - - -
441B GLY* 3.1 10.5 + - - +
443B GLY* 1.3 74.4 - - - +
445B ALA* 1.3 63.1 + - - +
447B MET* 3.3 4.1 + - + +
448B GLU* 2.9 47.4 + - - +
500B HEM 3.9 28.9 - - + -
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Residues in contact with ALA 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 4.0 13.9 - - + -
432B PHE* 3.7 27.4 - - + -
441B GLY 2.9 15.9 + - - +
442B GLU 3.7 0.2 - - - +
444B LEU* 1.3 77.5 - - - +
446B ARG* 1.3 57.3 + - - +
448B GLU* 3.1 3.8 + - - +
449B LEU* 2.8 36.0 + - - +
500B HEM 3.9 27.1 - - + +
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Residues in contact with ARG 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343B PHE* 3.9 13.4 - - + -
346B ARG* 4.9 10.7 - - - +
353B GLU* 4.4 10.7 + - - -
356B ILE* 5.7 4.9 - - - +
357B HIS* 3.6 35.4 + - - -
360B GLN* 3.9 21.5 + - - -
429B PHE* 4.8 6.4 - - - -
432B PHE* 4.0 11.3 - - + -
442B GLU* 2.9 49.5 + - + +
443B GLY* 4.0 5.6 - - - +
445B ALA* 1.3 72.0 - - - +
447B MET* 1.3 57.7 + - - +
449B LEU* 3.9 6.4 - - - +
450B PHE* 3.0 30.0 + - - +
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Residues in contact with MET 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B GLY* 4.4 24.9 - - - +
142B LYS 4.6 3.6 - - - +
145B ILE* 3.8 10.1 - - + -
146B GLU* 3.7 28.7 - - + +
149B ILE* 3.6 20.0 - - + -
343B PHE* 3.5 46.6 - - + -
443B GLY 3.1 18.1 + - - +
444B LEU* 3.7 4.7 - - - +
446B ARG* 1.3 74.3 - - - +
448B GLU* 1.3 60.1 + - - +
450B PHE* 3.4 0.5 + - - +
451B LEU* 2.9 48.9 + - + +
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Residues in contact with GLU 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 3.9 20.9 - - + -
178B VAL* 3.7 14.6 - - - +
181B VAL* 3.4 28.0 - - - +
182B ILE 4.8 0.5 + - - -
302B GLY 4.5 5.9 - - - +
306B VAL* 3.5 30.2 - - + +
444B LEU* 2.9 33.2 + - - +
445B ALA* 3.1 6.5 + - - +
447B MET* 1.3 75.0 - - - +
449B LEU* 1.3 60.1 + - - +
452B PHE* 2.8 60.2 + - + +
500B HEM 4.9 0.5 - - - +
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B VAL* 4.0 18.8 - - + -
309B THR* 3.7 26.7 - - + -
310B LEU* 3.8 22.4 - - + -
356B ILE* 4.2 15.7 - - + -
360B GLN* 3.7 38.1 - - + +
432B PHE* 5.0 0.7 - - + -
445B ALA 2.8 25.3 + - - +
446B ARG* 3.9 7.4 - - - +
448B GLU* 1.3 74.0 - - - +
450B PHE* 1.3 57.3 + - - +
453B PHE* 3.0 41.1 + - + +
500B HEM 4.1 10.8 - - + -
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B PRO* 4.7 2.7 - - + -
342B LYS 3.6 22.4 - - - -
343B PHE* 4.2 19.5 - + + -
345B ASP* 4.2 2.7 - - + -
346B ARG* 3.7 35.2 - - + -
349B MET* 3.8 18.2 - - + -
352B MET* 3.8 14.6 - - + -
353B GLU* 3.8 18.6 - - - +
356B ILE* 3.6 15.8 - - + +
446B ARG 3.0 17.8 + - - +
447B MET 4.0 2.2 - - - +
449B LEU* 1.3 77.7 - - - +
451B LEU* 1.3 73.9 + - + +
454B THR* 2.9 60.4 + - + +
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Residues in contact with LEU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B GLU* 4.2 18.6 - - + +
149B ILE* 3.4 35.9 - - + -
150B GLN* 4.4 6.7 - - + -
153B ALA* 4.5 2.6 - - + +
341B PRO* 3.5 28.9 - - + +
342B LYS* 3.7 23.3 - - - -
343B PHE* 3.7 2.2 - - - +
447B MET* 2.9 38.9 + - + +
450B PHE* 1.3 81.4 - - + +
452B PHE* 1.3 60.3 + - + +
454B THR* 4.0 1.3 - - - -
455B THR* 2.5 36.6 + - - +
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Residues in contact with PHE 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B ILE* 3.9 19.3 - - + -
152B GLU* 4.7 0.9 - - + -
153B ALA* 3.8 31.0 - - + -
156B LEU* 4.8 8.3 - - + -
177B THR* 3.4 32.1 - - + -
178B VAL* 4.3 10.8 - - + -
181B VAL* 3.9 15.3 - - + -
306B VAL* 5.0 0.2 - - + -
310B LEU* 4.0 32.3 - - + -
314B PHE* 5.3 0.9 - - + -
448B GLU* 2.8 58.5 + - + +
451B LEU* 1.3 72.8 - - - +
453B PHE* 1.3 62.7 + - - +
455B THR* 4.2 1.2 - - - -
456B VAL* 3.2 30.8 + - + +
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
309B THR* 3.8 2.5 - - + -
310B LEU* 3.7 40.6 - - + -
313B GLY* 3.7 27.1 - - - -
314B PHE* 3.9 28.9 - + - -
317B LEU* 4.7 8.5 - - + -
352B MET* 4.5 6.7 - - + -
356B ILE* 3.9 31.0 - - + -
359B ILE* 3.7 23.1 - - + -
449B LEU* 3.0 37.6 + - + +
452B PHE* 1.3 79.0 - - - +
454B THR* 1.3 61.1 + - - +
456B VAL* 4.0 0.7 - - - +
457B MET* 3.0 33.6 + - + +
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Residues in contact with THR 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B ILE* 3.6 7.0 - - - +
335B ILE* 4.8 4.3 - - - -
341B PRO* 3.0 29.1 - - - +
349B MET* 4.7 2.5 - - + -
352B MET* 3.3 42.6 - - + -
450B PHE* 2.9 41.7 + - + +
451B LEU 3.7 1.0 + - - -
453B PHE* 1.3 74.4 - - + +
455B THR* 1.3 63.3 + - - +
458B GLN* 2.8 31.9 + - - +
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Residues in contact with THR 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B ALA* 4.0 23.2 - - + +
157B ILE* 3.9 23.8 - - + -
340B GLN* 4.5 16.0 + - + -
341B PRO* 3.4 30.2 + - + +
451B LEU* 2.5 25.7 + - - +
452B PHE 4.2 1.1 - - - -
454B THR* 1.3 79.0 + - - +
456B VAL* 1.3 61.8 + - - +
458B GLN* 3.2 2.8 + - - +
459B ASN* 2.9 37.0 + - - +
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Residues in contact with VAL 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156B LEU* 3.8 27.8 - - + -
157B ILE* 3.8 15.0 - - + -
160B LEU* 4.2 7.6 - - + -
314B PHE* 3.5 35.2 - - + -
452B PHE* 3.2 20.0 + - + +
453B PHE 4.0 0.9 - - - +
455B THR* 1.3 75.9 - - - +
457B MET* 1.3 62.9 + - - +
459B ASN 3.1 1.9 + - - -
460B PHE* 2.8 30.1 + - + +
462B LEU* 4.6 2.0 - - + -
491B PHE* 3.8 25.6 - - + -
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Residues in contact with MET 457 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B PHE* 4.0 15.3 - - + -
317B LEU* 4.2 15.7 - - + -
324B GLU* 3.4 43.1 - - + +
327B VAL* 4.1 16.8 - - + -
328B HIS* 2.9 40.6 + - + -
331B ILE* 3.6 18.6 - - + -
352B MET* 4.7 1.8 - - + -
453B PHE* 3.0 26.0 + - + +
456B VAL* 1.3 73.5 - - - +
458B GLN* 1.3 64.7 + - - +
460B PHE 3.3 4.4 - - - +
462B LEU* 3.7 30.1 - - + -
494B ARG* 3.4 1.6 + - - -
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Residues in contact with GLN 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331B ILE* 3.7 20.4 - - + +
332B ASP* 5.6 0.7 - - - +
335B ILE* 3.5 11.7 - - - +
336B GLY 2.8 27.3 + - - +
337B LYS* 4.4 16.9 + - + +
339B ARG 3.0 23.3 + - - +
340B GLN* 4.1 4.0 - - - +
341B PRO* 3.4 22.6 - - + +
454B THR 2.8 22.8 + - - +
455B THR* 3.2 4.3 + - - +
457B MET* 1.3 73.9 - - - +
459B ASN* 1.3 74.9 + - - +
494B ARG* 3.1 26.6 + - - +
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Residues in contact with ASN 459 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157B ILE* 3.9 25.8 - - + +
161B ARG* 3.7 23.6 + - - +
340B GLN* 5.9 1.2 - - - +
455B THR* 2.9 27.9 + - - +
456B VAL 3.1 2.2 + - - -
458B GLN* 1.3 97.2 + - - +
460B PHE* 1.3 85.7 + - + +
494B ARG* 3.5 20.7 + - - +
496B HIS 5.4 2.9 - - - +
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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