Contacts of the helix formed by residues 615 - 626 (chain D) in PDB entry 1V40
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 ALA 615 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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606D LEU* 4.3 9.2 - - + -
608D TYR* 3.5 40.2 - - + -
612D ARG 3.3 0.2 + - - -
613D GLY 3.2 1.4 - - - -
614D ARG* 1.3 76.2 - - - +
616D GLU* 1.3 65.7 + - - +
617D ILE 3.2 3.1 - - - -
618D ILE* 2.9 20.5 + - - +
619D ARG* 3.1 24.5 + - - +
652D PRO* 4.0 13.9 - - + -
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Residues in contact with GLU 616 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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612D ARG* 3.0 39.5 + - + +
613D GLY 3.8 8.5 - - - +
614D ARG 3.5 0.8 - - - -
615D ALA* 1.3 76.9 - - - +
617D ILE* 1.3 63.3 + - - +
619D ARG* 2.9 32.2 + - - +
620D TYR* 2.9 37.6 + - + -
633D ARG* 4.8 1.0 + - - -
755D ILE* 3.7 17.3 - - + -
790D TRP* 2.8 32.2 + - - -
794D ARG* 2.8 23.0 + - - +
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Residues in contact with ILE 617 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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613D GLY 5.0 0.2 + - - -
614D ARG 3.9 17.6 + - - +
616D GLU* 1.3 77.7 - - - +
618D ILE* 1.3 74.2 + - + +
620D TYR* 3.3 1.0 + - - +
621D ILE* 3.1 29.3 + - + +
664D SER* 4.5 4.9 - - - +
665D LEU* 4.7 5.4 - - + -
668D ALA* 4.1 11.9 - - + -
748D TRP* 3.7 38.1 - - + +
751D PHE* 3.6 31.4 - - + -
752D TYR* 3.8 36.6 - - + +
755D ILE* 3.4 11.3 - - + +
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Residues in contact with ILE 618 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D LEU* 4.1 26.0 - - + -
615D ALA* 2.9 11.3 + - - +
617D ILE* 1.3 82.6 - - + +
619D ARG* 1.3 62.0 + - - +
621D ILE* 3.2 10.5 + - - +
622D PHE* 3.0 48.3 + - + -
652D PRO* 4.3 8.7 - - + -
654D LEU* 5.1 0.9 - - + -
664D SER* 3.9 22.9 - - - +
667D ILE* 3.6 42.6 - - + -
668D ALA* 4.3 5.4 - - - +
671D LEU* 3.8 9.9 - - + -
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Residues in contact with ARG 619 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606D LEU* 3.7 11.1 - - + +
608D TYR* 3.9 16.6 - - - +
609D PHE 3.6 15.0 + - - -
611D MET 3.0 26.7 + - - -
612D ARG* 3.4 8.5 + - - +
615D ALA* 3.1 14.8 + - - +
616D GLU* 2.9 29.7 + - - +
618D ILE* 1.3 77.0 - - - +
620D TYR* 1.3 61.6 + - - +
622D PHE* 3.6 2.7 + - - +
623D ALA* 3.1 23.0 + - - +
629D TYR* 3.4 22.9 + - - +
631D ASP* 2.7 26.0 + - - -
632D HIS 5.4 0.4 + - - -
633D ARG* 3.2 21.9 - - - +
790D TRP* 3.4 38.0 - - + +
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Residues in contact with TYR 620 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616D GLU* 2.9 40.3 + - + +
617D ILE 3.6 9.4 - - - +
618D ILE 3.2 0.2 - - - -
619D ARG* 1.3 76.7 - - - +
621D ILE* 1.3 57.7 + - - +
623D ALA* 3.2 6.8 + - - +
624D TYR* 2.9 31.2 + - - +
751D PHE* 3.9 33.1 - + + -
754D GLU* 2.6 36.6 + - - -
755D ILE* 3.5 22.5 - - + +
758D THR* 5.3 0.7 + - - -
781D VAL* 4.6 3.1 - - + -
787D VAL* 4.1 25.2 - - + +
790D TRP* 3.6 17.9 - + - -
791D ILE* 3.8 10.7 - - + +
794D ARG* 3.2 20.8 + - - -
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Residues in contact with ILE 621 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617D ILE* 3.1 21.9 + - + +
618D ILE* 3.2 8.0 + - - +
620D TYR* 1.3 74.1 - - - +
622D PHE* 1.3 66.1 + - + +
624D TYR* 3.4 4.7 + - - +
625D LEU* 3.0 46.3 + - + +
668D ALA* 3.6 42.8 - - + +
671D LEU* 3.8 21.3 - - + -
672D THR* 3.6 20.2 - - + -
677D LEU* 4.4 2.9 - - + -
748D TRP* 4.3 6.7 - - + -
751D PHE* 4.5 14.8 - - + -
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Residues in contact with PHE 622 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D TYR* 3.9 28.0 - + - -
606D LEU* 4.9 0.4 - - + -
618D ILE* 3.0 40.3 + - + -
619D ARG 3.8 3.4 - - - +
621D ILE* 1.3 77.2 - - + +
623D ALA* 1.3 62.4 + - - +
625D LEU* 3.5 0.8 + - - -
626D ASP* 3.0 3.3 + - - -
627D ILE* 2.9 65.7 + - + +
629D TYR* 3.5 54.5 - + + -
654D LEU* 4.0 12.6 - - + -
671D LEU* 3.7 29.2 - - + -
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Residues in contact with ALA 623 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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619D ARG 3.1 13.2 + - - +
620D TYR* 3.5 9.0 - - - +
622D PHE* 1.3 80.4 - - - +
624D TYR* 1.3 63.4 + - - +
626D ASP* 3.0 14.8 + - - +
629D TYR* 5.3 1.0 - - - -
786D ALA* 3.6 23.0 - - - +
787D VAL* 5.2 1.8 - - - -
790D TRP* 3.9 30.1 - - + -
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Residues in contact with TYR 624 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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620D TYR 2.9 16.8 + - - +
621D ILE 3.8 3.1 - - - +
623D ALA* 1.3 78.0 - - - +
625D LEU* 1.3 68.2 + - + +
626D ASP* 3.4 1.9 + - - +
676D ASP* 2.5 40.0 + - - -
677D LEU* 3.4 24.2 - - + -
746D VAL* 4.0 20.2 - - + +
751D PHE* 3.6 27.1 - + + -
784D ILE* 4.1 26.2 - - + -
786D ALA* 4.0 14.3 - - + +
787D VAL* 4.6 3.1 - - + +
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Residues in contact with LEU 625 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621D ILE* 3.0 32.9 + - + +
622D PHE 4.2 0.2 - - - +
624D TYR* 1.3 96.3 - - + +
626D ASP* 1.3 71.9 + - - +
627D ILE* 3.5 31.8 - - + +
671D LEU* 3.5 25.6 - - + +
675D THR* 4.1 31.6 - - + +
676D ASP* 4.6 3.4 - - - +
677D LEU* 4.4 2.9 - - + -
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Residues in contact with ASP 626 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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622D PHE 3.0 6.4 + - - -
623D ALA* 3.0 11.8 + - - +
624D TYR 3.2 2.0 - - - +
625D LEU* 1.3 81.8 - - - +
627D ILE* 1.3 60.6 + - - +
628D GLN* 4.2 13.1 + - - +
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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
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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