Contacts of the helix formed by residues 596 - 609 (chain B) in PDB entry 4P3N
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 SER 596 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455B VAL* 5.6 1.7 - - - +
458B PHE* 3.6 37.2 - - - +
459B GLN 3.4 8.3 - - - -
460B GLN* 3.7 1.8 - - - +
461B ASP 4.7 0.7 - - - +
594B LEU* 3.2 10.3 + - - +
595B GLY* 1.3 74.8 - - - -
597B VAL* 1.3 63.9 + - - +
598B GLU* 3.6 4.4 + - - +
599B ARG* 3.0 30.2 + - - +
600B MET* 3.1 18.2 + - - +
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Residues in contact with VAL 597 (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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353B TYR* 3.6 50.0 - - + +
356B LEU* 4.4 7.8 - - + +
357B ILE* 4.0 24.2 - - + -
437B PHE* 5.3 7.2 - - + -
459B GLN* 2.9 23.2 + - + +
460B GLN* 4.6 0.2 - - - +
461B ASP* 5.5 3.6 - - + +
594B LEU* 5.1 13.0 - - + -
596B SER* 1.3 71.4 - - - +
598B GLU* 1.3 60.4 + - - +
600B MET* 3.4 5.9 + - - +
601B ILE* 2.9 41.5 + - + +
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Residues in contact with GLU 598 (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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343B CYS* 5.4 2.5 - - + -
345B PHE* 4.5 5.1 - - + -
353B TYR* 2.6 34.3 + - + -
452B LEU* 3.5 41.3 - - + +
455B VAL* 5.1 4.5 - - + -
457B ARG* 3.1 23.6 + - - +
458B PHE* 3.3 23.1 - - + +
459B GLN 3.1 15.6 + - - -
596B SER* 3.2 4.7 - - - +
597B VAL* 1.3 79.7 + - - +
599B ARG* 1.3 62.0 + - - +
601B ILE* 3.2 10.1 + - - +
602B ALA 3.1 18.5 + - - -
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Residues in contact with ARG 599 (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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452B LEU 4.0 14.6 + - - +
453B THR* 4.4 25.4 + - + +
556B HIS* 3.8 23.6 + - - +
557B GLN* 2.6 38.2 + - - +
558B CYS* 4.0 8.0 - - - -
594B LEU 4.8 1.8 - - - +
595B GLY* 5.7 2.5 - - - -
596B SER* 3.0 24.7 + - - +
598B GLU* 1.3 78.5 - - - +
600B MET* 1.3 64.6 + - - +
602B ALA* 3.4 3.3 + - - +
603B ILE* 3.1 46.3 + - + +
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Residues in contact with MET 600 (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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356B LEU* 4.6 6.1 - - + -
487B TYR* 5.8 3.8 - - + -
490B PHE* 3.6 21.3 - - + -
492B PHE* 3.4 22.9 - - + -
548B ILE* 6.3 0.9 - - - -
558B CYS* 4.7 13.2 - - - -
594B LEU* 3.5 40.5 + - + +
596B SER 3.1 15.5 + - - +
597B VAL* 3.8 5.4 - - - +
599B ARG* 1.3 79.2 - - - +
601B ILE* 1.3 57.7 + - - +
603B ILE* 4.7 8.3 - - + -
604B LEU* 3.0 76.3 + - + +
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Residues in contact with ILE 601 (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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333B TYR* 3.7 29.4 - - + -
345B PHE* 3.5 25.4 - - + -
349B GLY* 4.5 2.7 - - - +
352B ILE* 4.4 10.5 - - + -
353B TYR* 3.8 31.6 - - + +
356B LEU* 3.7 16.6 - - + -
452B LEU* 3.8 7.4 - - + -
597B VAL* 2.9 25.5 + - + +
598B GLU 3.2 5.1 + - - +
600B MET* 1.3 74.1 - - - +
602B ALA* 1.3 56.2 + - - +
604B LEU* 3.4 4.6 + - - +
605B THR* 2.5 41.3 + - - +
612B TRP* 4.3 6.4 - - + -
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Residues in contact with ALA 602 (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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323B HIS* 3.4 45.7 - - + +
452B LEU* 3.7 22.0 - - + +
453B THR* 4.5 10.1 - - + -
598B GLU 3.1 5.7 + - - -
599B ARG 3.8 7.2 - - - +
601B ILE* 1.3 77.3 - - - +
603B ILE* 1.3 64.4 + - - +
605B THR* 3.1 4.7 + - - -
606B GLU* 3.0 22.7 + - - +
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Residues in contact with ILE 603 (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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453B THR* 5.6 5.8 - - + -
492B PHE* 4.5 20.0 - - + -
548B ILE* 5.3 2.0 - - + -
550B ASP* 5.2 1.7 - - + +
556B HIS* 3.7 56.5 - - + +
558B CYS* 4.3 12.6 - - - -
599B ARG* 3.1 41.1 + - + +
600B MET* 4.0 7.9 - - - +
602B ALA* 1.3 77.5 - - + +
604B LEU* 1.3 57.6 + - - +
606B GLU* 3.4 7.1 + - - +
607B ASN* 2.9 30.0 + - + +
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Residues in contact with LEU 604 (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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356B LEU* 4.2 11.7 - - + -
490B PHE* 3.7 12.8 - - + -
492B PHE* 3.9 17.3 - - + -
600B MET* 3.0 54.3 + - + +
601B ILE* 3.9 3.4 - - - +
603B ILE* 1.3 74.0 - - - +
605B THR* 1.3 60.3 + - - +
607B ASN* 4.2 2.5 - - - +
608B TYR* 2.9 59.8 + - + +
612B TRP* 4.0 14.8 - - + -
616B LEU* 3.7 27.6 - - + -
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Residues in contact with THR 605 (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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323B HIS* 3.6 19.1 - - - +
326B ILE* 3.4 33.1 - - + +
327B GLY 4.7 0.4 - - - +
332B LEU* 4.9 2.0 - - + -
333B TYR* 3.2 27.4 + - + +
601B ILE* 2.5 26.0 + - - +
602B ALA 3.1 4.7 + - - -
604B LEU* 1.3 76.4 - - - +
606B GLU* 1.3 62.2 + - - +
608B TYR* 5.2 0.2 - - - -
609B GLY 3.4 14.4 + - - -
610B GLY 3.7 3.3 + - - +
612B TRP* 3.5 26.0 - - + -
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Residues in contact with GLU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B ASP* 3.2 39.6 + - - +
323B HIS* 3.2 40.1 + - + -
453B THR* 5.9 2.1 - - - +
556B HIS* 5.8 4.7 - - - -
602B ALA 3.0 12.7 + - - +
603B ILE* 3.9 5.3 - - - +
605B THR* 1.3 76.8 - - - +
607B ASN* 1.3 62.9 + - - +
609B GLY* 3.5 10.0 + - - -
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Residues in contact with ASN 607 (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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490B PHE 5.1 2.6 + - - -
492B PHE* 3.6 26.1 - - + -
550B ASP* 3.2 13.7 - - + +
551B ALA* 2.5 50.4 + - - +
603B ILE 2.9 20.0 + - - +
604B LEU* 3.9 5.4 - - - +
606B GLU* 1.3 78.1 - - - +
608B TYR* 1.3 83.1 + - - +
609B GLY* 3.5 0.5 + - - -
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Residues in contact with TYR 608 (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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489B VAL 4.9 1.2 + - - -
490B PHE* 3.6 39.3 + - - -
604B LEU* 2.9 45.4 + - + +
605B THR* 4.7 0.7 - - - +
607B ASN* 1.3 92.1 - - - +
609B GLY* 1.3 63.7 + - - +
610B GLY 4.3 2.7 - - - +
611B LYS* 3.0 46.6 + - - +
612B TRP* 3.8 15.3 - + + -
613B PRO* 3.4 36.7 - - + +
616B LEU* 4.2 7.0 - - + -
717B LYS* 5.7 4.4 - - + +
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Residues in contact with GLY 609 (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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322B ASP* 5.8 0.4 - - - -
326B ILE* 4.3 11.0 - - - -
605B THR 3.4 9.9 + - - -
606B GLU 3.5 6.7 + - - -
607B ASN 3.2 4.6 + - - -
608B TYR* 1.3 77.7 - - - +
610B GLY* 1.3 56.4 + - - +
611B LYS* 3.4 8.8 + - - +
669B GLN* 4.9 3.5 + - - -
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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
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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