Contacts of the helix formed by residues 583 - 602 (chain B) in PDB entry 5NC5
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 THR 583 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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220A GLY 5.7 0.2 - - - +
224A PRO* 6.4 0.9 - - - -
228A GLN* 3.0 27.9 + - + +
229A GLN 3.4 33.0 - - - +
230A LEU 3.7 15.5 - - - +
231A ASN* 4.2 4.5 - - + +
581B GLY 4.0 1.3 - - - +
582B ALA* 1.3 77.2 - - - +
584B GLN* 1.3 67.7 + - - +
585B GLU* 4.0 4.6 + - - +
586B ARG* 3.2 32.5 + - - +
587B THR* 3.2 15.2 + - - -
622B GLN* 3.5 11.2 - - - +
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Residues in contact with GLN 584 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A THR* 4.3 5.2 - - - +
223A PRO* 5.2 0.2 - - - +
224A PRO* 3.3 33.7 - - + +
275B TYR 3.4 21.4 + - - +
276B ASP 3.7 10.9 - - - +
278B ILE* 3.2 32.3 - - + +
583B THR* 1.3 71.7 - - - +
585B GLU* 1.3 61.8 + - - +
587B THR* 3.3 2.3 + - - -
588B GLN* 3.1 8.2 + - - +
613B ASN* 2.9 41.5 + - - +
622B GLN* 2.7 38.7 + - + +
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Residues in contact with GLU 585 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A PRO* 5.7 4.8 - - + +
225A VAL 5.3 1.6 - - - +
226A LYS* 3.1 25.7 - - - +
227A GLY* 3.0 40.9 + - - -
228A GLN* 4.6 5.1 - - + +
229A GLN* 5.7 0.7 + - - -
583B THR* 3.1 7.6 + - - +
584B GLN* 1.3 76.6 - - - +
586B ARG* 1.3 66.4 + - + +
588B GLN* 3.2 8.7 + - + +
589B LYS* 3.2 38.5 + - - +
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Residues in contact with ARG 586 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A GLN 5.6 0.2 - - - +
229A GLN* 3.2 42.6 + - - +
578B LEU* 3.7 15.8 - - + +
579B PRO* 4.3 17.8 - - - +
581B GLY 4.3 1.8 + - - -
582B ALA* 3.6 31.5 - - - +
583B THR* 3.2 20.1 + - - +
585B GLU* 1.3 77.5 - - + +
587B THR* 1.3 64.4 + - - +
589B LYS* 3.1 17.6 + - - +
590B VAL* 3.3 13.7 + - - +
660B ASP* 5.5 7.3 + - - +
45D VAL* 5.1 7.5 - - - +
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Residues in contact with THR 587 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B VAL* 4.4 12.1 - - + -
578B LEU* 3.6 13.2 - - + +
583B THR 3.2 5.2 + - - -
584B GLN 3.6 7.9 - - - -
586B ARG* 1.3 79.1 - - - +
588B GLN* 1.3 62.8 + - - +
590B VAL* 3.2 4.0 + - - +
591B LEU* 3.0 29.5 + - + +
613B ASN* 3.7 15.5 - - - +
622B GLN 2.9 17.4 + - - -
623B ASN* 3.5 12.8 - - - -
624B THR* 3.6 28.0 - - - +
625B GLY 4.3 1.3 - - - +
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Residues in contact with GLN 588 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278B ILE* 3.8 21.8 + - + +
280B GLU* 3.3 38.6 + - - +
584B GLN 3.1 7.8 + - - +
585B GLU* 3.6 11.4 - - + +
586B ARG 3.2 0.6 - - - -
587B THR* 1.3 78.9 - - - +
589B LYS* 1.3 56.7 + - - +
591B LEU* 3.3 12.9 + - - +
592B ASN* 2.8 55.6 + - - +
611B ALA* 5.0 4.6 - - - +
613B ASN* 3.2 29.7 + - - +
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Residues in contact with LYS 589 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
585B GLU* 3.2 30.0 + - - +
586B ARG* 3.1 11.7 + - - +
588B GLN* 1.3 77.0 - - - +
590B VAL* 1.3 62.0 + - + +
592B ASN* 3.4 11.1 + - + +
593B GLU* 3.1 23.4 + - - +
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Residues in contact with VAL 590 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B VAL* 3.8 21.5 - - + -
578B LEU* 3.7 23.6 - - + -
586B ARG 3.4 15.0 - - - +
587B THR 3.2 5.3 + - - +
589B LYS* 1.3 74.7 - - + +
591B LEU* 1.3 63.2 + - - +
593B GLU* 3.2 8.1 + - - +
594B VAL* 2.9 34.1 + - + +
658B ILE* 4.1 19.5 - - + -
660B ASP 5.7 0.2 - - - +
661B ALA* 4.1 9.2 - - + -
663B VAL* 3.9 19.1 - - + -
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Residues in contact with LEU 591 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
576B VAL* 4.0 16.8 - - + +
587B THR* 3.0 26.4 + - + +
588B GLN* 3.8 10.5 - - - +
590B VAL* 1.3 77.6 - - - +
592B ASN* 1.3 59.0 + - - +
594B VAL* 3.4 5.2 + - - +
595B THR* 3.0 33.5 + - - -
611B ALA* 3.9 16.8 - - + -
612B VAL 4.3 1.1 - - - +
613B ASN* 3.6 42.6 - - + +
625B GLY* 4.6 1.3 - - - -
626B ILE 3.9 9.6 - - - +
627B ALA* 3.8 37.4 - - + +
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Residues in contact with ASN 592 (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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280B GLU* 3.4 13.6 + - - +
588B GLN* 2.8 52.0 + - - +
589B LYS* 3.7 11.8 - - + +
591B LEU* 1.3 74.3 - - - +
593B GLU* 1.3 56.8 + - - +
595B THR* 3.5 6.4 + - - -
596B HIS* 3.0 29.5 + - - +
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Residues in contact with GLU 593 (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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589B LYS 3.1 17.5 + - - +
590B VAL* 3.2 7.6 + - - +
592B ASN* 1.3 73.4 - - - +
594B VAL* 1.3 66.0 + - - +
596B HIS* 3.4 10.2 + - + +
597B TYR* 3.1 22.5 + - - +
655B PHE* 5.0 1.2 - - - -
658B ILE* 3.9 37.9 - - + +
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Residues in contact with VAL 594 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B THR* 4.1 5.4 - - - +
576B VAL* 4.5 6.7 - - + -
590B VAL* 2.9 23.3 + - + +
591B LEU* 3.6 8.1 - - - +
592B ASN 3.3 0.2 - - - -
593B GLU* 1.3 74.9 - - - +
595B THR* 1.3 66.5 + - - +
597B TYR* 3.1 12.8 + - - +
598B TYR* 3.2 46.7 + - + -
627B ALA* 3.9 20.4 - - + -
655B PHE* 3.9 18.2 - - + -
658B ILE* 4.5 7.2 - - + -
663B VAL* 3.8 28.0 - - + -
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Residues in contact with THR 595 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ASN* 4.6 10.5 - - - -
283B GLY* 4.9 5.6 - - - +
591B LEU 3.0 17.6 + - - -
592B ASN* 3.8 7.7 + - - -
594B VAL* 1.3 75.9 - - - +
596B HIS* 1.3 63.2 + - - +
598B TYR* 3.2 2.9 + - - +
599B LEU* 3.0 40.7 + - + +
609B VAL* 3.0 44.2 + - + +
611B ALA* 4.1 10.2 - - - +
627B ALA* 4.8 0.5 - - - +
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Residues in contact with HIS 596 (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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592B ASN 3.0 18.3 + - - +
593B GLU* 3.6 10.5 - - + +
594B VAL 3.2 0.2 - - - -
595B THR* 1.3 77.1 - - - +
597B TYR* 1.3 64.2 + - - +
599B LEU* 3.4 4.6 + - - +
600B THR* 2.9 53.4 + - + +
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Residues in contact with TYR 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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593B GLU 3.1 14.0 + - - +
594B VAL 3.1 6.5 + - - +
596B HIS* 1.3 79.6 - - - +
598B TYR* 1.3 83.7 + + - +
600B THR* 4.4 4.0 - - - -
601B LYS* 2.8 60.2 + - + +
602B GLU* 3.5 22.4 + - + -
650B ARG* 3.8 7.1 + - - +
651B ALA* 3.5 28.5 + - + -
654B ALA* 3.8 21.0 - - + +
655B PHE* 3.6 26.2 - + + -
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Residues in contact with TYR 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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572B PHE* 3.7 24.3 - + - -
574B THR* 3.1 24.9 - - + +
594B VAL* 3.2 44.9 + - + -
595B THR 3.2 4.4 + - - +
597B TYR* 1.3 97.0 - + - +
599B LEU* 1.3 63.7 + - - +
600B THR 3.2 0.9 + - - -
602B GLU* 3.3 34.3 + - + +
606B VAL* 3.8 18.4 - - + +
609B VAL* 3.9 20.0 - - + -
629B VAL* 3.7 22.0 - - + -
647B ILE* 4.9 2.0 - - + -
651B ALA* 3.7 13.6 - - + +
655B PHE* 3.3 19.5 - + - -
665B ALA* 4.0 0.9 - - - +
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Residues in contact with LEU 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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282B ASN* 3.5 39.7 - - + +
595B THR* 3.0 31.8 + - + +
596B HIS* 4.3 4.3 - - - +
598B TYR* 1.3 74.6 - - - +
600B THR* 1.3 58.6 + - - +
603B LYS* 3.6 20.6 - - - +
606B VAL* 3.7 28.7 - - + +
607B GLU 4.7 4.7 - - - +
609B VAL* 4.3 4.0 - - + -
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Residues in contact with THR 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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596B HIS* 2.9 47.0 + - + +
597B TYR* 3.8 2.2 - - - +
598B TYR 3.1 0.8 - - - -
599B LEU* 1.3 78.9 + - - +
601B LYS* 1.3 92.6 + - + +
602B GLU 3.4 0.9 - - - -
603B LYS* 3.6 16.2 - - - +
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Residues in contact with LYS 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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597B TYR* 2.8 46.2 + - + +
600B THR* 1.3 98.9 - - + +
602B GLU* 1.3 63.0 - - + +
603B LYS 3.5 1.3 + - - -
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Residues in contact with GLU 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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597B TYR* 3.5 34.3 + - + +
598B TYR* 3.3 22.1 + - + +
601B LYS* 1.3 80.3 - - - +
603B LYS* 1.3 65.6 + - - +
604B ASN* 3.0 4.3 - - - -
605B ASN* 2.6 48.4 + - + +
606B VAL* 3.1 20.3 + - + +
647B ILE* 3.6 27.5 - - + +
650B ARG* 3.5 25.3 + - - -
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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