Contacts of the helix formed by residues 537 - 559 (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 SER 537 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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533B GLY 3.2 16.3 + - - -
534B ILE 3.2 4.1 + - - -
535B LEU 3.2 1.2 - - - -
536B ARG* 1.3 79.7 - - - +
538B THR* 1.3 65.1 + - - +
539B GLY 3.2 3.4 + - - -
540B ARG* 3.7 13.2 + - - +
541B TYR* 3.5 15.2 - - - -
37H SER 3.4 27.9 + - - -
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Residues in contact with THR 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE 4.0 4.0 - - - -
535B LEU* 3.5 27.4 - - + +
536B ARG 5.2 0.2 - - - -
537B SER* 1.3 71.3 - - - +
539B GLY* 1.3 69.3 + - - +
540B ARG 3.4 0.2 - - - -
541B TYR* 3.1 16.7 + - - +
542B LEU* 3.2 17.1 + - - +
1024B VAL* 4.6 9.0 - - + -
1027B VAL* 4.5 5.8 - - + -
1028B VAL* 3.9 29.7 - - + +
1031B ARG* 3.6 20.4 + - - +
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Residues in contact with GLY 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B SER 3.2 1.8 - - - -
538B THR* 1.3 84.0 + - - +
540B ARG* 1.3 62.0 + - - +
542B LEU* 3.2 19.3 + - - +
543B VAL* 3.3 18.1 + - - +
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Residues in contact with ARG 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B SER* 3.8 15.7 - - - +
538B THR 3.4 0.2 - - - -
539B GLY* 1.3 72.8 - - - +
541B TYR* 1.3 59.9 + - + +
543B VAL* 3.5 9.6 + - - +
544B LEU* 3.0 24.8 + - - +
35H ILE 4.8 0.8 + - - -
36H PHE* 2.7 64.5 + - + -
37H SER* 3.0 37.2 + - - -
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Residues in contact with TYR 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B ILE* 3.5 48.1 - - + +
537B SER* 3.5 25.6 - - - -
538B THR* 3.1 7.4 + - - +
540B ARG* 1.3 76.3 - - + +
542B LEU* 1.3 59.6 + - - +
543B VAL 3.2 0.7 - - - -
544B LEU* 3.5 7.7 - - + +
545B TYR* 2.8 29.8 + - - +
1021B PHE* 3.7 18.8 - + + -
1024B VAL* 4.6 12.8 - - + -
33H PHE* 2.6 64.5 + + - -
36H PHE* 3.5 21.2 - + - -
37H SER 3.7 12.5 + - - -
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B THR* 3.2 16.0 + - - +
539B GLY* 3.2 10.3 + - - +
541B TYR* 1.3 76.3 - - - +
543B VAL* 1.3 63.2 + - + +
545B TYR* 3.5 8.3 + - + +
546B LEU* 3.1 33.6 + - + +
1024B VAL* 4.1 13.0 - - + -
1025B PHE* 5.1 12.8 - - + -
1028B VAL* 4.1 37.2 - - + -
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Residues in contact with VAL 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539B GLY 3.3 15.2 + - - +
540B ARG* 3.6 9.4 - - - +
541B TYR 3.2 0.4 - - - -
542B LEU* 1.3 75.1 - - + +
544B LEU* 1.3 66.2 + - - +
546B LEU* 3.3 12.4 + - + +
547B ILE* 3.0 32.5 + - + +
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Residues in contact with LEU 544 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B ARG 3.0 14.6 + - - +
541B TYR* 3.2 13.0 + - + +
543B VAL* 1.3 77.0 - - - +
545B TYR* 1.3 54.9 + - - +
547B ILE* 3.3 16.7 + - + +
548B ILE* 3.0 37.7 + - + +
1021B PHE* 4.4 12.6 - - + -
33H PHE* 4.2 21.8 - - + -
36H PHE* 3.9 25.4 - - + -
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Residues in contact with TYR 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B TYR 2.8 16.8 + - - +
542B LEU* 3.5 9.9 - - + +
544B LEU* 1.3 74.1 - - - +
546B LEU* 1.3 79.2 + - + +
548B ILE* 3.3 12.8 + - + +
549B VAL* 2.9 40.0 + - + +
903B LEU* 2.6 52.6 + - + +
906B PRO* 3.7 13.3 - - + +
907B LEU* 3.9 20.4 - - + -
1021B PHE* 4.1 11.4 - + + -
1025B PHE* 3.2 34.8 - + + -
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Residues in contact with LEU 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542B LEU* 3.1 21.3 + - + +
543B VAL* 3.3 13.7 + - + +
545B TYR* 1.3 98.1 - - + +
547B ILE* 1.3 66.3 + - + +
549B VAL* 3.4 8.3 + - + +
550B VAL* 3.0 34.3 + - + +
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Residues in contact with ILE 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543B VAL* 3.0 25.7 + - + +
544B LEU* 3.3 23.1 - - + +
546B LEU* 1.3 75.8 - - + +
548B ILE* 1.3 66.5 + - + +
550B VAL* 3.1 7.1 + - - +
551B GLY* 2.8 21.5 + - - -
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Residues in contact with ILE 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LEU* 3.0 29.1 + - + +
545B TYR* 3.3 11.0 - - + +
547B ILE* 1.3 78.6 - - + +
549B VAL* 1.3 52.4 + - - +
551B GLY* 3.1 2.1 + - - -
552B MET* 2.7 33.8 + - - +
906B PRO* 4.7 8.5 - - + +
907B LEU* 4.7 14.8 - - + -
910B ILE* 3.8 35.0 - - + +
1017B LEU* 4.5 13.7 - - + -
1021B PHE* 3.9 30.7 - - + -
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Residues in contact with VAL 549 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
545B TYR* 2.9 37.6 + - + +
546B LEU* 3.7 12.1 - - + +
547B ILE 3.3 0.2 - - - -
548B ILE* 1.3 74.1 - - - +
550B VAL* 1.3 65.6 + - + +
552B MET* 3.1 18.4 + - + +
553B ALA* 2.9 26.0 + - + +
906B PRO* 3.6 31.6 - - + -
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Residues in contact with VAL 550 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546B LEU* 3.0 21.9 + - + +
547B ILE* 3.6 5.4 - - - +
549B VAL* 1.3 79.0 - - + +
551B GLY* 1.3 64.6 + - - +
553B ALA* 3.2 8.0 + - + +
554B TYR* 2.8 31.3 + - + +
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Residues in contact with GLY 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
547B ILE 2.8 13.6 + - - -
548B ILE* 3.5 4.3 - - - -
550B VAL* 1.3 77.9 - - - +
552B MET* 1.3 56.5 + - - +
554B TYR* 3.8 9.0 - - - +
555B LEU* 2.9 36.6 + - - +
910B ILE* 3.9 7.4 - - - -
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Residues in contact with MET 552 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548B ILE 2.7 17.0 + - - +
549B VAL* 3.2 19.5 - - + +
551B GLY* 1.3 75.0 - - - +
553B ALA* 1.3 79.4 + - + +
555B LEU* 3.6 2.1 - - - +
556B PHE* 2.9 35.8 + - + +
905B VAL* 6.2 0.9 - - - -
906B PRO* 3.9 28.0 - - + +
909B VAL* 3.8 32.5 - - + -
910B ILE* 3.6 19.9 - - + +
913B LEU* 3.7 8.5 - - + +
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Residues in contact with ALA 553 (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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549B VAL* 2.9 13.5 + - + +
550B VAL* 3.6 9.2 - - - +
552B MET* 1.3 86.7 - - + +
554B TYR* 1.3 65.3 + - - +
556B PHE* 3.1 6.4 + - - +
557B VAL* 2.9 28.8 + - + +
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Residues in contact with TYR 554 (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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550B VAL* 2.8 23.4 + - + +
551B GLY* 3.8 8.1 - - - +
553B ALA* 1.3 75.0 - - - +
555B LEU* 1.3 77.3 + - + +
556B PHE 3.2 0.2 + - - -
557B VAL* 3.2 13.5 + - + +
558B ARG* 2.7 57.3 + - + +
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Residues in contact with LEU 555 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551B GLY* 2.9 24.9 + - - +
552B MET 3.6 3.8 - - - +
554B TYR* 1.3 90.4 - - + +
556B PHE* 1.3 63.7 + - - +
558B ARG* 3.3 16.0 + - - +
559B LEU* 3.4 13.7 + - - +
910B ILE* 3.8 16.4 - - + -
913B LEU* 4.0 19.9 - - + +
914B LEU* 3.2 34.8 - - + -
917B THR* 3.8 29.9 + - + +
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Residues in contact with PHE 556 (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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552B MET* 2.9 23.2 + - + +
553B ALA* 3.1 9.8 + - - +
555B LEU* 1.3 76.1 - - - +
557B VAL* 1.3 70.8 + - + +
558B ARG 3.1 1.2 + - - -
559B LEU* 3.2 19.1 + - - +
909B VAL* 5.0 5.2 - - + -
913B LEU* 3.8 30.1 - - + -
923B ASN* 4.0 25.6 + - - -
931B LEU* 4.4 19.7 - - + -
1111B D10 5.2 13.2 - - + -
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Residues in contact with VAL 557 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
553B ALA* 2.9 18.3 + - + +
554B TYR* 3.2 8.9 + - + +
556B PHE* 1.3 85.3 - - + +
558B ARG* 1.3 63.3 + - + +
559B LEU 3.5 1.4 - - - +
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Residues in contact with ARG 558 (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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554B TYR* 2.7 54.2 + - + +
555B LEU* 3.3 13.7 + - - +
556B PHE 3.0 0.6 - - - -
557B VAL* 1.3 82.3 - - + +
559B LEU* 1.3 62.6 + - - +
560B PRO* 3.3 9.7 - - - +
917B THR* 5.7 10.1 - - + -
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Residues in contact with LEU 559 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555B LEU 3.4 8.0 + - - +
556B PHE* 3.2 17.6 + - - +
557B VAL 5.0 1.4 - - - +
558B ARG* 1.3 75.6 - - - +
560B PRO* 1.3 79.6 - - + +
561B SER* 3.6 2.3 + - - -
913B LEU* 4.1 21.1 - - + -
916B ALA* 4.1 18.8 - - + -
917B THR* 4.1 31.4 - - + +
920B GLY* 6.1 0.2 - - - -
921B LEU 3.2 24.7 - - - +
922B THR 4.2 1.1 - - - -
923B ASN* 4.0 33.0 + - + +
927B PHE* 4.3 7.2 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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