Contacts of the helix formed by residues 599 - 614 (chain B) in PDB entry 1LD7
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 599 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129A ALA* 6.1 0.7 - - - +
596B LEU* 3.0 23.7 + - - +
598B ALA* 1.3 82.8 + - - +
600B ARG* 1.3 65.7 + - - +
601B PRO* 3.3 6.3 - - - -
602B TRP* 3.0 30.1 + - - +
603B LEU* 3.3 7.2 + - - +
642B GLY* 4.4 0.4 - - - -
652B PRO* 5.2 0.4 - - - -
1003B U66 3.3 34.1 - - - -
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Residues in contact with ARG 600 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A GLN* 3.1 21.7 + - - +
82A ASP* 2.7 37.6 + - - +
87A VAL 3.1 24.4 + - - +
88A VAL* 3.2 18.4 + - + +
89A GLN* 3.9 7.9 - - - +
90A ILE* 4.1 9.1 - - + +
92A TYR* 3.8 2.4 + - - -
596B LEU 3.8 13.0 - - - +
597B ASP* 3.9 22.0 - - - +
599B SER* 1.3 73.3 - - - +
601B PRO* 1.3 70.5 - - + +
603B LEU* 3.1 26.8 + - + +
604B CYS* 3.1 15.9 + - - -
629B PHE* 3.2 34.8 - - + -
642B GLY 3.1 12.9 + - - +
643B GLY* 5.0 0.7 - - - -
644B PRO* 3.8 4.9 - - - +
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Residues in contact with PRO 601 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B SER 3.4 3.4 - - - -
600B ARG* 1.3 91.5 - - + +
602B TRP* 1.3 55.8 + - - +
604B CYS* 3.3 4.3 + - + +
605B TYR* 3.0 23.4 + - - +
629B PHE* 5.0 0.2 - - + -
630B LEU* 4.1 22.7 - - + -
633B CYS* 4.2 16.8 - - + -
640B PHE* 5.1 0.4 - - + -
641B GLY 3.3 21.8 - - - +
642B GLY* 3.4 15.7 - - - +
652B PRO* 3.6 28.9 - - + +
655B ALA* 3.6 10.8 - - - +
656B ALA* 4.1 7.5 - - + +
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Residues in contact with TRP 602 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B SER* 3.0 29.5 + - - +
601B PRO* 1.3 77.9 - - - +
603B LEU* 1.3 58.7 + - - +
605B TYR* 3.2 7.8 + + - +
606B TRP* 2.8 80.8 + + + -
651B ALA* 3.4 43.1 - - + +
652B PRO* 4.1 12.1 - - + +
654B TYR* 3.5 31.2 - + - -
655B ALA* 3.7 10.8 - - + -
865B TYR* 3.7 15.0 - - - -
1002B FPP 3.8 28.5 - - + -
1003B U66 3.5 33.8 - + - -
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Residues in contact with LEU 603 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 3.9 16.2 - - + -
90A ILE* 5.1 2.7 - - + -
589B LEU* 3.5 26.2 - - + -
593B TYR* 3.7 35.0 - - + -
596B LEU* 4.2 13.7 - - + +
599B SER 3.3 4.2 + - - +
600B ARG* 3.1 31.7 + - + +
602B TRP* 1.3 78.3 - - - +
604B CYS* 1.3 63.0 + - - +
606B TRP* 3.9 22.3 - - + +
607B ILE* 3.1 32.2 + - + +
860B PHE* 4.1 14.1 - - + -
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Residues in contact with CYS 604 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87A VAL* 4.3 7.9 - - - -
88A VAL* 3.9 26.9 - - - +
586B LEU* 4.8 5.8 - - - -
600B ARG 3.1 15.7 + - - -
601B PRO* 3.4 9.6 - - + +
603B LEU* 1.3 76.9 - - - +
605B TYR* 1.3 57.6 + - - +
607B ILE* 3.8 0.9 - - - +
608B LEU* 2.9 37.9 + - + +
626B VAL* 4.3 15.7 - - + -
629B PHE* 3.9 19.7 - - - -
630B LEU* 4.2 9.9 - - + -
659B ALA* 4.5 11.4 - - + -
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Residues in contact with TYR 605 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
601B PRO 3.0 12.5 + - - +
602B TRP* 3.7 16.6 - + - +
604B CYS* 1.3 73.9 - - - +
606B TRP* 1.3 83.5 + + - +
608B LEU* 4.7 0.7 - - - -
609B HIS* 2.9 41.6 + + + +
654B TYR* 4.3 5.5 + + - -
655B ALA* 3.5 24.9 - - + +
658B ASN* 3.5 38.1 + - + -
659B ALA* 4.2 9.1 - - + +
662B ILE* 3.9 7.9 - - + -
864B CYS* 4.2 3.4 - - - -
865B TYR* 3.7 20.3 + - - -
902B ASN* 2.8 49.8 + - - +
903B ILE* 3.9 3.8 - - + -
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Residues in contact with TRP 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LEU* 5.3 0.4 - - - -
593B TYR* 5.8 0.4 - + - -
596B LEU* 4.2 15.9 - - + -
602B TRP* 2.8 51.5 + + + +
603B LEU* 3.9 25.8 - - + +
605B TYR* 1.3 87.5 - + - +
607B ILE* 1.3 56.5 + - - +
609B HIS 4.1 0.2 - - - -
610B SER* 2.7 34.9 + - - -
860B PHE* 3.6 20.4 - - + +
861B TYR* 3.5 42.4 - + + -
864B CYS* 3.7 23.4 - - + +
865B TYR* 3.5 16.4 + + - -
1003B U66 3.5 45.1 - + - -
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Residues in contact with ILE 607 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A VAL* 4.5 4.5 - - + -
582B LEU* 3.5 28.0 - - + +
585B GLY 3.5 31.6 - - - +
586B LEU* 3.6 21.8 - - + +
589B LEU* 5.4 0.4 - - + -
603B LEU* 3.1 24.6 + - + +
604B CYS 3.9 1.8 - - - +
606B TRP* 1.3 74.0 - - - +
608B LEU* 1.3 65.5 + - - +
610B SER* 3.3 3.1 + - - -
611B LEU* 3.0 33.9 + - + +
860B PHE* 3.6 39.0 - - + -
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Residues in contact with LEU 608 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
586B LEU* 4.0 30.1 - - + -
604B CYS* 2.9 26.3 + - + +
605B TYR* 4.1 1.6 - - - +
607B ILE* 1.3 72.3 - - - +
609B HIS* 1.3 58.4 + - - +
611B LEU* 3.3 6.9 + - + +
612B GLU* 2.8 29.6 + - - +
618B ILE* 3.7 29.8 - - + +
626B VAL* 4.0 29.8 - - + -
659B ALA* 4.0 26.2 - - + +
662B ILE* 4.1 18.2 - - + +
663B ILE* 4.2 10.1 - - + -
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Residues in contact with HIS 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B TYR* 2.9 31.1 + - + +
606B TRP 4.2 2.2 - - - +
608B LEU* 1.3 75.0 - - - +
610B SER* 1.3 61.3 + - - +
612B GLU* 2.6 31.2 + - - -
613B LEU* 2.9 55.4 + - + +
662B ILE* 3.7 10.7 - - + +
864B CYS* 3.9 9.6 - - - -
868B SER* 3.2 20.9 + - - -
897B THR* 3.3 16.0 + - - -
902B ASN* 2.9 42.2 + - - -
903B ILE* 3.5 7.2 - - - -
904B GLY 4.3 0.4 - - - -
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Residues in contact with SER 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
582B LEU* 3.5 29.2 - - - +
606B TRP 2.7 23.2 + - - -
607B ILE 3.5 0.7 - - - -
608B LEU 3.2 0.2 - - - -
609B HIS* 1.3 75.4 - - - +
611B LEU* 1.3 60.1 + - - +
613B LEU* 3.3 7.0 + - - +
614B LEU* 3.0 32.9 + - - +
860B PHE 4.7 0.2 + - - -
863B THR* 3.8 4.7 - - - +
864B CYS* 3.3 25.0 + - - +
867B LEU* 3.9 14.7 - - - +
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Residues in contact with LEU 611 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
579B PHE* 3.7 33.9 - - + +
582B LEU* 3.8 26.9 - - + -
583B LYS* 4.8 3.8 - - - +
586B LEU* 4.3 16.4 - - + -
607B ILE* 3.0 35.2 + - + +
608B LEU* 3.6 12.6 - - + +
610B SER* 1.3 72.9 - - - +
612B GLU* 1.3 61.6 - - - +
614B LEU* 3.1 3.5 + - - -
615B ASP 2.9 9.9 + - - -
616B GLU* 2.9 43.8 + - + +
617B PRO 5.7 2.0 - - - +
618B ILE* 4.9 10.3 - - + -
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Residues in contact with GLU 612 (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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608B LEU 2.8 17.2 + - - +
609B HIS* 2.6 36.4 + - + +
611B LEU* 1.3 76.9 - - - +
613B LEU* 1.3 64.7 + - + +
615B ASP* 2.9 15.2 + - - +
616B GLU 4.9 2.9 - - - +
618B ILE* 5.7 3.3 - - + +
662B ILE* 3.8 22.0 - - + +
895B GLN* 3.5 14.4 - - + +
904B GLY* 2.8 33.7 + - - -
906B ASP* 4.5 1.0 - - - +
907B LYS* 3.2 22.7 - - - +
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Residues in contact with LEU 613 (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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575B ARG* 4.9 0.2 + - - -
609B HIS* 2.9 48.3 + - + +
610B SER* 3.3 5.8 + - - +
612B GLU* 1.3 77.0 - - + +
614B LEU* 1.3 57.8 + - + +
615B ASP* 3.1 3.5 + - - +
864B CYS 4.2 2.0 - - - +
867B LEU* 3.7 17.9 - - + -
868B SER* 3.5 40.2 - - - +
871B SER* 4.2 8.5 - - - -
894B LEU* 3.5 14.6 - - + +
895B GLN* 2.9 49.9 + - + +
896B PRO 4.4 3.1 - - - +
897B THR* 4.0 14.1 - - - -
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Residues in contact with LEU 614 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LEU* 4.0 14.1 - - + -
575B ARG* 3.0 43.8 + - + +
578B HIS* 4.1 14.6 - - + -
579B PHE 4.5 4.9 - - - +
582B LEU* 3.5 27.6 - - + -
610B SER 3.0 20.5 + - - +
611B LEU* 3.1 5.6 + - - +
613B LEU* 1.3 74.9 - - - +
615B ASP* 1.3 70.0 + - - +
616B GLU* 3.2 20.1 + - + +
867B LEU* 4.1 17.7 - - + -
894B LEU* 3.7 19.7 - - + -
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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
------------------------------------------------------------
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