Contacts of the helix formed by residues 577 - 590 (chain B) in PDB entry 5N4D
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 577 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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496B TYR* 4.4 9.4 - - - -
576B ALA* 1.3 70.7 - - - +
578B ASN* 1.3 70.1 + - - -
580B GLY 2.8 11.3 + - - +
581B LEU 3.1 9.2 + - - -
601B GLU 2.8 14.3 + - - -
602B GLY* 3.4 15.8 + - - -
603B GLY* 3.2 9.3 - - - -
604B VAL* 4.1 3.4 + - - -
664B VAL* 4.8 12.8 + - - +
12D GLU* 5.5 2.8 + - - -
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Residues in contact with ASN 578 (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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496B TYR* 2.9 47.5 + - + +
497B GLY 3.0 26.3 + - - -
498B GLY* 3.5 2.4 - - - +
499B PHE* 3.5 16.2 - - + -
546B LYS* 4.5 3.2 - - - +
549B THR* 5.6 0.2 - - - +
576B ALA 3.2 0.6 + - - -
577B SER* 1.3 81.7 - - - +
579B GLY* 1.3 56.8 + - - +
581B LEU* 3.3 8.8 + - - +
582B LEU* 2.9 22.8 + - - +
604B VAL* 6.4 0.7 - - - -
623B TYR* 2.4 40.1 + - - -
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Residues in contact with GLY 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B GLY 3.6 18.8 - - - +
496B TYR* 3.6 11.7 + - - -
575B GLY* 3.5 8.4 - - - -
576B ALA 2.8 18.9 + - - -
578B ASN* 1.3 78.4 - - - +
580B GLY* 1.3 58.5 + - - +
582B LEU* 3.4 3.9 - - - +
583B VAL* 3.0 32.7 + - - +
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Residues in contact with GLY 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B GLY 3.7 11.4 - - - -
576B ALA 3.5 4.4 - - - -
577B SER 2.8 11.0 + - - -
579B GLY* 1.3 74.9 - - - +
581B LEU* 1.3 58.9 + - - +
583B VAL 3.2 1.0 + - - -
584B MET* 2.9 42.1 + - - +
600B PRO* 3.7 12.5 - - - +
601B GLU 4.1 4.9 - - - -
603B GLY* 3.9 8.3 - - - -
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Residues in contact with LEU 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LYS* 5.4 3.8 - - + -
550B PHE* 3.5 20.0 - - + -
577B SER 3.1 9.6 + - - +
578B ASN* 3.4 11.9 - - - +
580B GLY* 1.3 74.5 - - - +
582B LEU* 1.3 56.6 + - - +
584B MET* 4.4 0.9 - - - -
585B GLY 2.8 27.4 + - - -
603B GLY* 3.7 3.0 - - - -
604B VAL* 3.2 34.1 - - + +
607B LEU* 4.4 20.0 - - + -
623B TYR* 3.7 38.8 - - + +
640B PRO* 3.6 29.2 - - + -
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Residues in contact with LEU 582 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B GLY* 3.6 38.4 - - - +
496B TYR 3.7 10.5 - - - +
527B ILE* 3.7 11.4 - - + -
549B THR* 3.8 28.7 - - + +
550B PHE* 3.5 17.0 - - + -
553B PHE* 3.7 36.1 - - + -
578B ASN* 2.9 14.4 + - - +
579B GLY 3.4 7.9 - - - +
580B GLY 3.2 0.2 - - - -
581B LEU* 1.3 76.1 - - - +
583B VAL* 1.3 56.7 + - + +
586B SER* 2.7 37.8 + - - +
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Residues in contact with VAL 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B PHE* 4.6 5.8 - - + -
573B ILE* 3.9 24.2 - - + -
574B ASN* 3.7 36.1 - - - +
575B GLY 3.7 1.8 - - - +
579B GLY 3.0 21.6 + - - +
580B GLY 3.2 3.8 + - - +
582B LEU* 1.3 77.0 - - + +
584B MET* 1.3 63.8 + - - +
586B SER* 3.2 1.6 + - - -
587B ILE* 3.0 26.1 + - + +
598B ALA* 3.9 17.7 - - + -
599B VAL 4.3 1.8 - - - +
600B PRO* 3.8 27.4 - - + -
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Residues in contact with MET 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
580B GLY 2.9 24.8 + - - +
581B LEU 4.0 2.2 - - - +
583B VAL* 1.3 77.0 - - - +
585B GLY* 1.3 63.4 + - - +
587B ILE* 3.5 8.5 - - + +
588B VAL* 3.5 22.7 + - - +
600B PRO* 3.6 25.1 - - + -
603B GLY* 3.7 27.8 - - - +
604B VAL 3.6 19.5 - - - +
605B ALA* 3.8 8.7 - - + -
640B PRO* 4.1 11.2 - - + -
655B ILE* 4.6 4.3 - - + -
669B SER* 4.4 10.3 - - - +
672B PHE* 3.4 49.4 - - + -
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Residues in contact with GLY 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B PHE* 3.6 22.4 - - - -
581B LEU 2.8 11.3 + - - -
584B MET* 1.3 76.1 - - - +
586B SER* 1.3 64.3 + - - +
588B VAL* 3.5 3.9 + - - +
589B ARG* 3.1 32.4 + - - +
638B LEU 5.1 2.5 - - - -
640B PRO* 3.7 17.5 - - - +
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Residues in contact with SER 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550B PHE* 3.7 12.3 + - - -
553B PHE* 3.5 17.5 - - - +
554B ILE* 4.2 14.2 - - - +
573B ILE* 4.0 9.2 - - - -
582B LEU* 2.7 25.5 + - - +
583B VAL 3.2 4.0 + - - -
585B GLY* 1.3 77.9 - - - +
587B ILE* 1.3 65.4 + - - +
590B ALA* 2.9 28.2 + - - +
595B PHE* 3.9 20.2 - - - -
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Residues in contact with ILE 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B ILE* 3.8 11.7 - - + -
583B VAL* 3.0 18.7 + - + +
584B MET* 3.5 13.9 - - - +
586B SER* 1.3 78.0 - - - +
588B VAL* 1.3 64.5 + - - +
590B ALA* 4.2 8.7 + - - +
595B PHE* 4.2 10.8 - - + -
598B ALA* 3.6 24.9 - - + -
600B PRO* 6.4 0.7 - - + -
650B MET* 3.4 37.6 - - + +
651B PRO* 3.8 18.4 - - + +
653B THR* 3.7 26.5 - - + +
672B PHE* 4.3 22.9 - - + -
676B LEU* 4.6 4.5 - - + -
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Residues in contact with VAL 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET 3.5 12.1 + - - +
585B GLY* 3.5 7.8 + - - +
586B SER 3.2 0.4 - - - -
587B ILE* 1.3 82.2 - - + +
589B ARG* 1.3 67.0 + - + +
640B PRO* 4.1 7.0 - - + +
643B ASN* 2.9 41.5 - - + +
644B VAL* 4.0 19.5 - - + +
645B ARG* 5.0 5.5 + - - +
648B LYS* 2.9 22.2 + - - +
650B MET* 4.8 8.5 - - - +
672B PHE* 3.9 24.7 - - + -
676B LEU* 5.5 0.2 - - + -
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Residues in contact with ARG 589 (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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468B LYS* 6.1 0.4 - - - +
547B VAL* 3.5 19.5 - - - +
550B PHE* 4.0 30.7 - - - +
551B ASP* 4.4 10.3 + - - -
554B ILE* 4.1 11.6 - - + +
585B GLY* 3.1 23.0 + - - +
588B VAL* 1.3 86.8 - - + +
590B ALA* 1.3 66.1 + - - +
591B PRO* 3.8 2.6 - - - +
637B PRO* 3.4 25.6 + - - +
638B LEU* 3.5 25.5 - - - +
643B ASN* 6.1 0.9 - - + -
648B LYS* 3.5 5.7 + - - -
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Residues in contact with ALA 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554B ILE* 4.0 17.7 - - + +
586B SER 2.9 17.9 + - - +
587B ILE 4.2 5.4 + - - +
588B VAL 3.6 0.2 - - - -
589B ARG* 1.3 78.1 - - - +
591B PRO* 1.3 76.6 - - + +
592B GLU* 4.4 0.2 - - - -
594B THR* 3.6 13.0 - - + +
595B PHE* 3.5 23.6 - - + -
648B LYS* 2.9 19.9 + - - -
650B MET* 5.8 0.2 - - - +
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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