Contacts of the helix formed by residues 569 - 584 (chain B) in PDB entry 1LV5
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 GLU 569 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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517B ARG* 2.6 34.2 + - - +
521B LEU* 4.2 5.4 - - + -
568B HIS* 1.3 87.6 + - + +
570B ILE* 1.3 60.1 + - - +
571B VAL 2.9 5.8 - - - -
572B GLU* 2.9 41.6 + - + +
573B ASN* 3.7 6.0 - - - +
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Residues in contact with ILE 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
517B ARG 4.4 0.2 - - - +
518B ILE* 3.3 30.1 - - + +
521B LEU* 3.4 39.1 - - + +
522B ALA* 3.8 16.2 - - + -
526B PHE* 5.3 1.1 - - + -
537B ILE* 5.1 3.1 - - + -
538B LEU* 6.0 2.2 - - + -
542B LEU* 3.6 25.4 - - + -
544B LEU* 5.4 0.7 - - + -
568B HIS* 3.1 21.4 + - + +
569B GLU* 1.3 76.7 - - - +
571B VAL* 1.3 68.9 + - + +
572B GLU 3.1 0.4 - - - -
573B ASN* 2.9 12.6 + - + +
574B ILE* 3.0 29.7 + - + +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
538B LEU* 6.0 1.8 - - + -
544B LEU* 4.6 0.4 - - + -
561B LEU* 2.6 45.8 - - + +
564B LEU* 3.5 21.8 - - + +
565B ALA* 3.4 32.8 - - + +
568B HIS* 3.9 23.3 - - + +
569B GLU 2.9 0.2 - - - -
570B ILE* 1.3 84.7 - - + +
572B GLU* 1.3 61.3 + - + +
574B ILE* 3.3 7.3 + - - +
575B LEU* 3.2 26.4 + - + +
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Residues in contact with GLU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
565B ALA* 5.3 8.3 - - + +
568B HIS 4.8 2.6 - - - +
569B GLU* 2.9 33.5 + - + +
571B VAL* 1.3 80.2 - - + +
573B ASN* 1.3 62.2 + - - +
574B ILE 3.3 0.2 - - - -
575B LEU* 4.6 5.5 - - - +
576B HIS* 2.9 27.5 + - - +
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Residues in contact with ASN 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B VAL* 3.8 10.9 - - - +
517B ARG* 2.9 45.8 + - - +
518B ILE* 2.8 46.2 - - + +
521B LEU* 3.0 19.1 - - - +
569B GLU* 3.7 4.7 - - - +
570B ILE* 2.9 10.5 + - - +
572B GLU* 1.3 79.5 + - - +
574B ILE* 1.3 58.6 + - - +
576B HIS* 3.9 7.8 + - - -
577B TYR 3.3 9.2 + - - -
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Residues in contact with ILE 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B ILE* 3.4 35.2 - - + -
526B PHE* 5.4 2.5 - - + -
528B ILE* 4.7 5.2 - - + -
534B LEU* 3.9 33.4 - - + -
538B LEU* 5.9 6.5 - - + -
561B LEU* 3.7 25.8 - - + -
570B ILE* 3.0 30.0 + - + +
571B VAL* 3.3 8.7 + - - +
573B ASN* 1.3 76.2 - - - +
575B LEU* 1.3 65.6 + - - +
576B HIS 3.1 1.3 - - - -
577B TYR* 3.2 5.5 + - - +
578B ARG* 3.2 31.2 + - + +
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Residues in contact with LEU 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558B ALA* 3.6 27.6 - - + -
561B LEU* 3.7 36.3 - - + +
562B GLU* 3.5 34.8 - - + +
565B ALA* 5.6 1.6 - - + -
571B VAL* 3.2 15.9 + - + +
572B GLU* 4.6 5.2 - - - +
574B ILE* 1.3 76.6 - - - +
576B HIS* 1.3 56.8 + - - +
578B ARG* 3.4 6.1 + - - +
579B GLN* 3.0 30.7 + - - +
26E G 4.5 6.7 - - - +
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Residues in contact with HIS 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B GLN* 3.5 16.5 + - - -
514B VAL* 3.2 40.5 - - + +
572B GLU 2.9 23.2 + - - +
573B ASN* 3.9 6.5 + - - +
574B ILE 3.1 0.4 - - - -
575B LEU* 1.3 78.5 - - - +
577B TYR* 1.3 60.0 - - - +
579B GLN* 3.7 17.4 + - - +
580B LEU* 3.1 48.4 + - + +
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Residues in contact with TYR 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LEU* 3.0 47.3 + - + +
514B VAL* 4.1 4.7 - - + +
515B GLU* 2.7 38.9 + - + -
518B ILE* 3.4 29.2 - - + -
528B ILE* 3.4 31.1 - - + +
529B ASN* 3.4 22.3 + - - -
573B ASN 3.3 3.8 + - - +
574B ILE* 3.2 6.8 + - - +
576B HIS* 1.3 81.3 - - - +
578B ARG* 1.3 56.5 + - + +
581B GLY* 2.8 33.8 + - - -
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Residues in contact with ARG 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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528B ILE 4.9 8.1 + - - +
531B PRO* 4.4 8.1 - - - +
534B LEU* 4.0 14.3 - - - +
556B THR* 2.6 54.0 + - - +
558B ALA 4.2 1.8 - - - +
561B LEU* 3.6 16.7 - - - +
574B ILE* 3.2 22.5 + - + +
575B LEU* 3.9 8.0 - - + +
576B HIS 3.4 0.2 - - - -
577B TYR* 1.3 80.3 - - + +
579B GLN* 1.3 63.5 + - - +
581B GLY* 4.9 0.9 - - - -
582B LYS* 3.2 26.9 + - - +
25E A 3.2 16.8 + - - -
26E G 3.0 40.2 + - - +
27E C 4.9 1.7 + - - -
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Residues in contact with GLN 579 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
575B LEU 3.0 18.1 + - - +
576B HIS* 3.7 21.6 + - - +
578B ARG* 1.3 79.1 - - - +
580B LEU* 1.3 81.3 + - - +
582B LYS* 3.5 2.8 + - - +
583B LEU* 2.9 37.7 - - + +
630B LEU* 4.0 26.1 - - + +
632B GLU* 4.0 30.5 - - - +
27E C 4.5 10.3 - - - +
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Residues in contact with LEU 580 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 3.7 28.4 - - + +
510B GLN* 3.6 26.7 - - + +
511B LEU* 3.2 29.7 - - + +
514B VAL* 3.6 24.5 - - + -
576B HIS* 3.1 40.5 + - + +
579B GLN* 1.3 93.0 - - - +
581B GLY* 1.3 63.9 + - - +
583B LEU* 3.1 17.6 + - + +
584B GLN* 3.3 9.9 + - - +
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Residues in contact with GLY 581 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
511B LEU* 3.3 17.8 - - - +
577B TYR* 2.8 26.1 + - - -
578B ARG* 4.1 0.9 - - - -
580B LEU* 1.3 75.0 - - - +
582B LYS* 1.3 58.7 + - - +
584B GLN* 4.3 0.5 - - - +
585B SER* 2.8 29.8 + - - -
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Residues in contact with LYS 582 (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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578B ARG 3.2 19.3 + - - +
579B GLN 4.0 3.8 - - - +
580B LEU 3.2 0.4 - - - -
581B GLY* 1.3 75.4 - - - +
583B LEU* 1.3 65.9 + - + +
585B SER* 4.4 2.5 - - - -
586B THR* 3.1 42.2 + - - +
587B TYR* 3.6 11.0 - - + -
25E A 4.8 4.6 + - - -
26E G 3.0 73.7 + - - +
27E C 3.2 33.0 - - - +
8F T 4.5 5.3 + - - -
9F G 6.0 0.4 + - - -
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Residues in contact with LEU 583 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507B LEU* 3.5 32.1 - - + -
579B GLN* 2.9 40.4 - - + +
580B LEU* 3.1 5.7 + - - +
582B LYS* 1.3 81.8 - - + +
584B GLN* 1.3 69.2 + - - +
587B TYR* 3.5 10.1 + - + +
588B ILE* 2.8 25.2 + - + +
627B PRO* 5.0 11.9 - - + -
630B LEU* 6.2 2.2 - - + -
632B GLU* 4.2 6.3 - - + +
633B GLY* 3.5 37.0 - - - +
636B ILE* 5.1 8.5 - - + +
27E C 5.4 7.0 - - - +
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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
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504B GLY* 2.7 34.8 + - - +
507B LEU* 4.2 8.9 - - + +
508B ALA* 3.9 16.3 - - - +
511B LEU* 4.2 17.5 - - + -
580B LEU 3.3 10.8 + - - +
581B GLY 3.8 2.0 + - - +
582B LYS 3.4 0.2 - - - -
583B LEU* 1.3 85.7 - - - +
585B SER* 1.3 70.9 + - - +
586B THR 2.7 2.1 + - - -
588B ILE* 3.0 38.1 + - - +
589B GLU* 3.1 32.3 + - + +
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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