Contacts of the helix formed by residues 689 - 708 (chain A) in PDB entry 4L6V
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 GLY 689 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A SER* 1.3 78.4 - - - +
690A ARG* 1.3 61.8 + - - -
691A GLY 3.1 7.4 + - - -
692A TYR* 3.4 12.5 + - - +
693A TRP* 3.1 18.9 + - - -
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Residues in contact with ARG 690 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A THR* 5.8 0.2 + - - -
689A GLY* 1.3 70.3 - - - -
691A GLY* 1.3 59.2 + - - +
692A TYR 3.3 0.2 - - - -
693A TRP* 3.5 11.2 - - - -
694A GLN* 2.7 75.3 + - - +
716A ARG* 4.4 8.9 - - - +
717A ALA* 3.2 21.6 + - + +
718A LEU 3.1 28.4 + - - +
719A SER* 4.4 2.5 - - - +
720A ILE* 3.9 34.0 - - + +
543B LEU* 5.0 10.1 - - - +
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Residues in contact with GLY 691 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
689A GLY* 3.1 2.0 - - - -
690A ARG* 1.3 85.0 - - - +
692A TYR* 1.3 61.6 + - - +
695A GLU* 3.6 25.7 + - - +
543B LEU* 4.0 15.8 - - - +
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Residues in contact with TYR 692 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688A SER* 5.9 4.0 - - - -
689A GLY 3.4 10.1 + - - +
690A ARG 3.3 0.4 - - - -
691A GLY* 1.3 74.9 - - - +
693A TRP* 1.3 103.9 + + + +
695A GLU* 3.3 7.4 + - - +
696A LEU* 3.1 31.0 + - + +
529B LEU* 4.6 3.3 - - - +
530B ILE* 3.5 50.0 + - + +
533B LYS* 3.4 44.8 - - + +
534B GLY* 5.7 0.7 - - - -
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Residues in contact with TRP 693 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
684A MET* 3.2 45.0 + - + -
685A PHE* 5.9 0.2 - - - +
688A SER* 2.8 28.7 + - - -
689A GLY 3.1 26.5 - - - -
690A ARG* 3.1 8.5 + - - +
692A TYR* 1.3 95.9 - + - +
694A GLN* 1.3 62.2 + - - +
696A LEU* 3.4 33.2 + - + +
697A ILE* 3.2 31.5 + - + +
717A ALA* 4.0 13.9 - - + -
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Residues in contact with GLN 694 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ARG* 2.7 43.7 + - - +
693A TRP* 1.3 70.2 - - - +
695A GLU* 1.3 65.9 + - - +
697A ILE* 3.3 15.5 + - - +
698A GLU* 3.2 33.3 + - - +
715A PRO 3.6 21.4 + - - -
716A ARG* 3.6 14.2 - - - +
717A ALA* 2.7 27.8 + - + +
543B LEU* 3.7 27.6 - - + -
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Residues in contact with GLU 695 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLY 3.6 14.5 + - - +
692A TYR* 3.3 9.0 + - - +
694A GLN* 1.3 78.1 - - - +
696A LEU* 1.3 63.3 + - - +
698A GLU* 3.3 23.5 + - - +
699A SER* 3.6 8.7 + - - -
533B LYS* 3.2 26.3 + - - +
537B ASP* 3.6 26.4 - - - +
540B GLY* 5.4 0.2 - - - -
541B SER* 2.5 38.4 + - - +
543B LEU* 4.6 9.9 - - + +
544B MET* 5.0 2.8 + - - -
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Residues in contact with LEU 696 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
692A TYR* 3.1 23.6 + - + +
693A TRP* 3.6 41.1 - - + +
695A GLU* 1.3 78.1 - - - +
697A ILE* 1.3 62.9 + - + +
699A SER* 3.2 15.2 + - - -
700A ILE* 3.2 30.1 + - + +
417B ILE* 3.9 20.4 - - + -
421B SER* 5.7 3.8 - - - +
529B LEU* 4.1 21.3 - - + -
533B LYS* 3.6 25.7 - - + +
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Residues in contact with ILE 697 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
693A TRP* 3.2 19.2 + - + +
694A GLN* 3.3 12.3 + - - +
696A LEU* 1.3 79.1 - - + +
698A GLU* 1.3 51.8 + - - +
700A ILE* 3.0 16.5 + - + +
701A VAL* 2.6 52.8 + - + +
715A PRO* 3.8 24.2 - - + +
716A ARG 4.2 4.0 - - - +
717A ALA* 3.6 36.1 - - + +
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Residues in contact with GLU 698 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694A GLN* 3.2 25.4 + - - +
695A GLU* 3.4 12.9 - - - +
696A LEU 3.2 0.4 - - - -
697A ILE* 1.3 75.8 - - - +
699A SER* 1.3 61.0 - - - +
701A VAL* 3.5 8.1 + - - +
702A TRP* 3.1 23.0 + - - +
414B GLU* 4.9 0.6 - - - +
537B ASP* 5.7 0.2 - - - +
541B SER* 3.4 11.2 - - - -
542B LYS* 3.4 48.3 + - + +
543B LEU* 3.5 29.1 + - - +
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Residues in contact with SER 699 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695A GLU 3.6 7.1 + - - -
696A LEU 3.2 10.6 + - - -
698A GLU* 1.3 78.9 - - - +
700A ILE* 1.3 62.8 + - - +
702A TRP* 3.5 14.7 + - - +
703A ALA 3.6 1.0 + - - -
413B LYS* 5.5 1.0 - - - +
414B GLU* 3.6 23.3 - - - +
417B ILE* 3.3 47.5 - - - +
418B SER* 3.4 17.7 - - - -
537B ASP* 4.6 2.6 + - - -
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Residues in contact with ILE 700 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696A LEU* 3.3 37.5 - - + +
697A ILE* 3.0 16.5 + - + +
699A SER* 1.3 75.9 - - - +
701A VAL* 1.3 67.3 + - + +
703A ALA* 3.1 10.9 + - + +
704A HIS* 3.1 35.0 + - + -
417B ILE* 5.9 0.4 - - + -
418B SER* 4.5 8.5 - - - +
421B SER* 4.3 24.9 - - - +
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Residues in contact with VAL 701 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
697A ILE* 2.6 40.9 + - + +
698A GLU* 3.7 8.1 - - - +
700A ILE* 1.3 71.6 - - + +
702A TRP* 1.3 59.1 + - - +
704A HIS* 2.8 26.7 + - - +
705A ASN* 3.0 29.9 + - - +
710A ALA* 5.1 6.5 - - + -
711A PRO* 5.9 2.0 - - + -
715A PRO* 3.8 28.0 - - + +
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Residues in contact with TRP 702 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698A GLU 3.1 14.4 + - - +
699A SER 3.5 8.3 - - - +
700A ILE 3.2 0.2 - - - -
701A VAL* 1.3 76.2 - - - +
703A ALA* 1.3 77.3 + - + +
705A ASN* 3.2 14.5 + - + +
706A LYS* 2.9 59.9 + - + +
412B HIS* 6.0 2.2 - - + -
414B GLU* 3.4 42.8 - - + +
415B ALA* 3.4 35.9 - - + -
418B SER* 3.8 7.4 - - - -
419B HIS* 4.5 8.1 - + - -
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Residues in contact with ALA 703 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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699A SER 3.6 0.4 + - - -
700A ILE* 3.1 12.7 + - + +
701A VAL 3.1 0.6 - - - -
702A TRP* 1.3 91.4 - - + +
704A HIS* 1.3 65.0 + - + +
706A LYS* 3.5 16.1 - - - +
707A LEU* 3.5 20.6 + - + +
418B SER* 4.0 24.2 - - - +
419B HIS* 5.8 2.2 - - + -
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Residues in contact with HIS 704 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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700A ILE* 3.1 31.9 + - + -
701A VAL* 2.8 12.0 + - - +
703A ALA* 1.3 80.8 - - + +
705A ASN* 1.3 55.0 + - - +
706A LYS 3.0 1.6 - - - -
707A LEU 3.2 0.3 + - - -
708A ASN 2.7 30.3 + - - -
709A VAL* 2.7 52.4 + - + +
710A ALA* 3.7 10.3 - - + +
711A PRO* 5.1 6.5 - - + -
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Residues in contact with ASN 705 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A VAL* 3.0 39.6 + - - +
702A TRP* 3.5 16.2 - - + +
704A HIS* 1.3 75.2 - - - +
706A LYS* 1.3 60.3 + - - +
707A LEU 3.6 0.2 + - - -
708A ASN* 3.6 9.2 + - - +
710A ALA* 4.2 16.6 - - - +
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Residues in contact with LYS 706 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702A TRP* 2.9 47.6 + - + +
703A ALA* 3.5 12.6 - - - +
704A HIS 3.0 0.2 - - - -
705A ASN* 1.3 80.6 - - - +
707A LEU* 1.3 67.8 + - + +
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Residues in contact with LEU 707 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703A ALA* 3.5 16.5 + - + +
704A HIS 3.2 2.2 + - - -
706A LYS* 1.3 86.9 - - + +
708A ASN* 1.3 71.3 + - - +
709A VAL* 3.3 24.4 + - + +
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Residues in contact with ASN 708 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704A HIS 2.7 7.9 + - - -
705A ASN* 3.6 9.1 + - - +
706A LYS 3.4 2.8 + - - -
707A LEU* 1.3 82.1 - - - +
709A VAL* 1.3 60.0 + - - +
710A ALA* 3.7 2.7 - - - +
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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