Contacts of the helix formed by residues 601 - 614 (chain A) in PDB entry 4Z96
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 601 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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600A SER* 1.3 76.1 + - - +
602A LEU* 1.3 59.4 + - - +
603A ALA* 3.6 3.8 + - - +
604A GLU* 2.6 40.8 + - - +
605A PHE* 2.9 28.2 + - - +
644A GLY 3.7 8.8 + - - -
645A ASN* 4.1 8.7 - - - -
646A LYS 3.3 13.7 - - - -
647A THR* 4.9 1.6 - - - -
648A MET* 4.0 4.3 - - - +
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Residues in contact with LEU 602 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A SER* 1.3 71.0 - - - +
603A ALA* 1.3 61.4 + - - +
605A PHE* 3.1 5.4 + - + -
606A VAL* 2.8 50.1 + - + +
622A LEU* 5.1 4.9 - - + -
638A LEU* 3.7 32.8 - - + -
639A ASP 4.2 0.7 - - - +
640A ASN* 3.8 22.9 - - + +
643A ASP 3.9 8.3 - - - +
644A GLY* 3.5 23.1 + - - +
646A LYS 3.2 6.5 + - - -
648A MET* 3.9 20.5 - - + -
651A LEU* 3.7 24.5 - - + -
658A TRP* 5.5 2.9 - - + -
660A ILE* 6.0 1.3 - - + -
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Residues in contact with ALA 603 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601A SER* 3.3 2.9 - - - +
602A LEU* 1.3 79.2 - - - +
604A GLU* 1.3 66.8 + - - +
606A VAL* 3.3 6.9 + - - +
607A GLN* 3.1 21.3 + - - +
617A GLN* 5.2 1.0 - - - +
640A ASN 5.4 4.7 - - - +
644A GLY* 3.4 18.6 + - - +
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Residues in contact with GLU 604 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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600A SER* 3.4 16.5 - - - -
601A SER* 2.6 49.3 + - - +
603A ALA* 1.3 79.6 - - - +
605A PHE* 1.3 63.9 + - - +
607A GLN* 3.2 3.6 + - - +
608A SER* 3.1 22.4 + - - -
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Residues in contact with PHE 605 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A VAL* 3.8 20.2 - - + -
569A ILE* 3.9 18.2 - - + -
594A PHE* 3.7 23.6 - + + -
596A VAL* 3.6 32.8 - - + -
600A SER* 5.4 2.4 + - - +
601A SER 2.9 15.3 + - - +
602A LEU* 3.1 6.2 + - + +
604A GLU* 1.3 76.7 - - - +
606A VAL* 1.3 60.9 + - + +
608A SER* 3.5 8.1 + - - -
609A LEU* 2.8 41.1 + - + +
622A LEU* 4.0 27.8 - - + -
648A MET* 3.6 31.4 - - + -
660A ILE* 4.4 2.0 - - + -
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Residues in contact with VAL 606 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602A LEU* 2.8 35.3 + - + +
603A ALA* 3.8 7.0 - - - +
604A GLU 3.2 0.2 - - - -
605A PHE* 1.3 77.9 - - + +
607A GLN* 1.3 58.5 + - - +
609A LEU* 3.4 7.6 + - - +
610A SER* 2.8 27.5 + - - -
617A GLN* 3.8 27.1 - - + +
620A ILE* 4.5 12.3 - - + +
622A LEU* 3.6 32.1 - - + -
640A ASN* 5.0 11.9 - - + +
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Residues in contact with GLN 607 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603A ALA 3.1 12.8 + - - +
604A GLU* 3.8 6.5 - - - +
606A VAL* 1.3 74.9 - - - +
608A SER* 1.3 66.6 + - - +
610A SER* 3.1 3.9 + - - -
611A GLN* 2.9 27.3 + - + +
617A GLN* 3.5 29.9 + - - +
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Residues in contact with SER 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A PHE* 5.1 7.7 - - - -
604A GLU 3.1 11.1 + - - -
605A PHE* 3.5 15.0 - - - -
607A GLN* 1.3 80.4 - - - +
609A LEU* 1.3 61.4 + - - -
611A GLN* 3.4 6.8 + - - +
612A THR* 3.1 27.4 + - - -
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Residues in contact with LEU 609 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A ILE* 3.9 11.9 - - + -
594A PHE* 3.5 39.0 - - + -
605A PHE* 2.8 31.6 + - + +
606A VAL* 3.4 5.2 - - - +
608A SER* 1.3 73.1 - - - +
610A SER* 1.3 62.6 + - - +
612A THR* 2.9 2.9 + - - -
613A MET* 2.8 48.1 + - + +
620A ILE* 3.6 29.6 - - + -
622A LEU* 4.4 16.4 - - + -
662A LEU* 3.6 18.4 - - + -
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Residues in contact with SER 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606A VAL 2.8 20.1 + - - -
607A GLN* 3.3 6.5 - - - -
609A LEU* 1.3 73.0 - - - +
611A GLN* 1.3 57.1 + - - +
613A MET* 5.0 0.9 - - - -
614A GLY* 3.0 8.7 + - - -
615A PHE* 2.2 59.1 + - - +
616A PRO* 3.7 1.2 - - - +
617A GLN* 3.5 29.1 + - - +
620A ILE* 4.4 12.6 - - - -
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Residues in contact with GLN 611 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607A GLN* 2.9 16.3 + - + +
608A SER* 3.6 9.8 - - - +
610A SER* 1.3 78.6 + - - +
612A THR* 1.3 74.0 + - - +
614A GLY* 3.5 7.8 + - - -
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Residues in contact with THR 612 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A THR* 5.3 4.3 - - + -
594A PHE* 4.0 29.4 - - + -
608A SER* 3.1 14.2 + - - -
609A LEU 2.9 6.6 + - - -
611A GLN* 1.3 88.0 + - - +
613A MET* 1.3 65.2 + - + +
614A GLY* 4.5 0.3 - - - -
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Residues in contact with MET 613 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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569A ILE* 3.5 33.0 - - + -
592A THR* 3.9 30.3 - - - +
594A PHE* 4.2 4.5 - - + -
609A LEU* 2.8 44.8 + - + +
610A SER* 4.4 1.1 - - - +
612A THR* 1.3 74.5 - - - +
614A GLY* 1.3 61.4 + - - +
615A PHE* 3.9 28.3 - - + -
662A LEU* 3.6 17.0 - - + -
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Residues in contact with GLY 614 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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610A SER 3.0 7.2 + - - -
611A GLN 3.5 6.7 + - - -
612A THR 3.3 3.6 - - - -
613A MET* 1.3 79.7 - - - +
615A PHE* 1.3 67.5 + - - +
616A PRO* 4.3 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
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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