Contacts of the helix formed by residues 598 - 610 (chain A) in PDB entry 1N35
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 PHE 598 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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425A LEU* 3.5 24.7 - - + -
592A SER 3.7 16.4 - - - -
593A ILE* 4.0 20.6 - - + -
594A THR 3.3 8.0 + - - +
597A PHE* 1.3 95.3 - + + +
599A LEU* 1.3 64.0 + - - +
601A VAL* 2.9 6.9 + - - +
602A ILE* 2.8 33.4 + - + +
694A ASN* 3.9 22.4 - - - -
698A MET* 4.1 16.4 - - + -
767A PHE* 3.8 25.8 - + - -
769A TRP* 3.1 46.9 - + - -
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Residues in contact with LEU 599 (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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542A HIS* 4.0 25.6 - - + -
593A ILE* 3.7 37.7 - - + +
594A THR* 3.0 21.0 + - - +
595A TRP* 3.8 17.3 - - + +
598A PHE* 1.3 73.3 - - - +
600A SER* 1.3 57.0 + - - +
602A ILE* 4.3 6.3 - - + +
603A MET* 2.8 35.7 + - + +
655A TYR* 3.8 35.0 - - + +
678A THR 5.9 0.9 - - - +
680A PHE* 3.9 12.8 - - + -
690A GLU* 4.3 4.3 - - - +
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Residues in contact with SER 600 (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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404A TRP* 3.6 29.1 - - - -
411A ILE* 5.6 0.5 - - - +
412A ARG 4.5 1.7 + - - +
595A TRP* 2.7 66.4 + - - -
596A ASP* 4.1 5.9 + - - -
597A PHE 4.3 0.5 + - - -
599A LEU* 1.3 75.9 - - - +
601A VAL* 1.3 64.5 + - - +
603A MET* 4.3 0.9 - - - +
604A ALA* 3.3 22.3 + - - +
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Residues in contact with VAL 601 (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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399A ILE* 3.7 13.2 - - + -
404A TRP* 3.6 22.4 - - + -
414A LEU* 4.7 3.1 - - + -
422A ALA* 4.2 10.3 - - + +
425A LEU* 3.8 14.1 - - + -
426A TYR* 3.5 42.5 - - + +
597A PHE 3.1 20.0 - - - +
598A PHE 2.9 7.3 + - - +
600A SER* 1.3 77.1 + - - +
602A ILE* 1.3 66.5 + - - +
604A ALA* 3.1 6.2 + - - +
605A ALA* 2.9 22.5 + - - +
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Residues in contact with ILE 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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425A LEU* 4.5 6.5 - - + -
429A TRP* 3.5 45.3 - - + +
542A HIS* 4.1 12.6 - - + +
598A PHE* 2.8 34.0 + - + +
599A LEU* 4.0 9.2 - - + +
601A VAL* 1.3 74.6 - - - +
603A MET* 1.3 66.7 + - + +
605A ALA* 3.3 4.7 + - - +
606A ILE* 3.1 33.8 + - + +
690A GLU* 3.1 26.2 - - - +
694A ASN* 3.4 21.3 - - - +
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Residues in contact with MET 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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411A ILE* 4.4 4.0 - - + -
542A HIS* 4.9 4.9 - - - -
595A TRP* 3.7 20.6 - - + -
599A LEU* 2.8 30.2 + - - +
600A SER 4.3 0.2 - - - +
602A ILE* 1.3 77.1 - - - +
604A ALA* 1.3 57.9 + - - +
606A ILE* 4.0 1.7 - - - +
607A HIS* 3.0 32.1 + - - +
648A ILE* 3.0 41.2 - - + +
651A LEU* 3.5 19.7 - - + -
652A SER* 2.8 42.0 - - - +
655A TYR* 3.7 25.8 - - + -
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Residues in contact with ALA 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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404A TRP* 4.8 1.3 - - + -
411A ILE* 4.6 11.2 - - + +
412A ARG 3.5 24.0 - - - +
413A ILE* 4.6 2.7 - - + -
426A TYR* 3.6 17.0 - - + -
600A SER 3.3 18.6 + - - +
601A VAL* 3.1 6.6 + - - +
603A MET* 1.3 80.2 - - - +
605A ALA* 1.3 63.6 + - - +
607A HIS* 3.3 5.3 + - - +
608A GLU* 3.0 29.1 + - - +
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Residues in contact with ALA 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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426A TYR* 3.2 46.6 - - + +
429A TRP* 3.8 11.9 - - + -
430A TYR* 3.4 20.1 - - + +
601A VAL 2.9 18.4 + - - +
602A ILE 3.9 0.9 - - - +
604A ALA* 1.3 73.2 - - - +
606A ILE* 1.3 54.2 + - - +
609A GLY* 2.7 33.1 + - - -
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Residues in contact with ILE 606 (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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429A TRP* 3.8 20.4 - - + +
433A ALA* 3.7 7.4 - - + -
541A PRO* 4.2 8.3 - - + -
542A HIS* 3.9 22.4 - - + +
545A THR* 3.8 27.4 - - + +
602A ILE* 3.1 35.2 + - + +
603A MET* 4.0 3.1 - - - +
605A ALA* 1.3 73.2 - - - +
607A HIS* 1.3 68.7 + - - +
610A VAL* 2.9 42.3 + - + +
644A MET* 5.9 0.2 - - + -
648A ILE* 3.7 26.7 - - + -
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Residues in contact with HIS 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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408A ILE* 4.2 17.0 - - + -
411A ILE* 4.1 13.3 - - + +
603A MET 3.0 20.8 + - - +
604A ALA* 3.6 5.8 - - - +
606A ILE* 1.3 78.6 - - - +
608A GLU* 1.3 83.6 + - - +
610A VAL* 5.0 0.4 - - - -
611A ALA 3.8 1.9 + - - -
639A ARG* 5.4 1.8 - - - -
641A ILE* 3.9 14.3 - - + +
645A GLN* 2.7 83.2 + - + +
648A ILE* 3.7 18.1 - - + +
649A GLN* 3.3 25.6 + - - -
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Residues in contact with GLU 608 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408A ILE* 4.3 2.6 - - - +
411A ILE* 4.5 1.5 - - + +
413A ILE* 3.0 38.2 - - + +
426A TYR* 3.8 13.5 - - - +
430A TYR* 3.7 20.5 + - + -
604A ALA 3.0 19.3 + - - +
607A HIS* 1.3 105.4 + - - +
609A GLY* 1.3 62.8 + - - +
610A VAL 3.0 4.9 - - - -
611A ALA* 3.0 24.4 + - - +
612A SER 4.8 0.2 + - - -
639A ARG* 4.0 16.9 + - - -
645A GLN* 4.6 1.7 + - - -
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Residues in contact with GLY 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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430A TYR* 3.3 33.3 - - - -
433A ALA* 4.1 0.4 - - - -
434A ALA* 2.9 33.0 - - - +
605A ALA 2.7 21.9 + - - -
606A ILE 3.9 0.2 - - - -
608A GLU* 1.3 74.9 - - - +
610A VAL* 1.3 58.2 + - - +
611A ALA 3.7 0.2 + - - -
612A SER* 5.1 5.4 + - - -
613A SER* 5.7 0.5 + - - -
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Residues in contact with VAL 610 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433A ALA* 3.5 29.4 - - + +
436A MET* 5.2 2.7 - - - -
437A ALA* 3.8 13.7 - - + +
541A PRO* 6.0 0.2 - - + -
545A THR* 5.1 1.8 - - - +
606A ILE* 2.9 31.0 + - + +
607A HIS* 4.5 0.7 - - - +
609A GLY* 1.3 77.4 - - - +
611A ALA* 1.3 60.0 + - - +
612A SER 3.7 0.9 - - - -
613A SER* 3.6 3.2 + - - -
614A SER* 2.7 43.0 + - - +
644A MET* 3.3 34.8 - - + -
645A GLN* 4.4 9.9 - - + +
648A ILE* 6.5 0.7 - - + -
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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