Contacts of the helix formed by residues 711 - 726 (chain W) in PDB entry 5IY8
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 ASP 711 (chain W).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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497W ARG* 3.2 39.0 + - - +
526W GLU* 5.2 0.3 - - - +
709W THR* 3.1 17.1 + - - -
710W VAL* 1.4 81.8 - - + +
712W GLU* 1.3 66.7 + - - +
713W GLY* 3.0 17.8 + - - -
714W VAL* 3.4 28.8 + - + +
715W GLN* 3.3 15.1 + - - +
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Residues in contact with GLU 712 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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492W PRO* 3.7 24.0 - - + -
493W MET* 3.1 32.8 + - - +
494W ILE* 3.8 15.0 - - + +
495W ILE 5.5 0.3 + - - -
497W ARG* 5.5 7.0 - - - +
523W LEU* 6.0 0.7 - - + -
527W MET* 4.0 19.5 - - + -
707W ASN 4.3 6.4 - - - +
709W THR* 3.3 32.1 + - + +
710W VAL 5.5 0.3 - - - -
711W ASP* 1.3 73.8 + - - +
713W GLY* 1.3 67.0 + - - +
715W GLN* 3.1 3.1 + - - +
716W VAL* 3.0 28.6 + - + +
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Residues in contact with GLY 713 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
526W GLU* 6.0 1.8 - - - -
527W MET* 4.7 11.3 - - - +
530W VAL* 4.9 13.1 - - - +
531W VAL* 4.3 9.2 - - - +
711W ASP* 3.0 8.3 + - - -
712W GLU* 1.3 79.6 - - - +
714W VAL* 1.3 62.0 + - - +
716W VAL* 3.4 11.8 - - - +
717W ALA* 3.2 22.7 + - - +
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Residues in contact with VAL 714 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
711W ASP* 3.4 31.3 + - + +
713W GLY* 1.3 77.7 - - - +
715W GLN* 1.4 58.4 + - - +
717W ALA* 3.3 6.1 + - - +
718W LYS* 2.9 56.3 + - + +
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Residues in contact with GLN 715 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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490W LEU* 4.2 15.3 - - + -
492W PRO* 6.4 0.7 - - + -
709W THR* 2.8 36.8 + - + +
710W VAL* 5.8 0.2 - - - +
711W ASP 3.3 10.1 + - - +
712W GLU* 3.1 9.8 + - - +
714W VAL* 1.4 80.5 - - - +
716W VAL* 1.4 51.1 + - + +
718W LYS* 3.4 22.1 + - - +
719W TYR* 2.8 35.3 + - - +
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Residues in contact with VAL 716 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
490W LEU* 3.8 14.1 - - + -
492W PRO* 4.2 12.1 - - + -
527W MET* 5.6 6.3 - - + -
531W VAL* 3.6 30.5 - - + -
676W LEU* 3.7 35.4 - - + -
678W VAL* 5.2 1.3 - - + -
712W GLU* 3.0 13.6 + - + +
713W GLY* 3.4 14.4 - - - +
715W GLN* 1.4 70.9 - - + +
717W ALA* 1.3 63.2 + - - +
719W TYR* 3.3 8.1 + - - +
720W PHE* 2.8 36.7 + - + -
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Residues in contact with ALA 717 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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530W VAL* 6.4 0.9 - - + -
531W VAL* 5.2 7.6 - - + -
713W GLY 3.2 18.1 + - - +
714W VAL* 3.8 5.6 - - - +
716W VAL* 1.3 76.7 - - + +
718W LYS* 1.3 61.2 + - + +
720W PHE* 3.2 12.4 + - - +
721W LEU* 3.0 31.5 + - + +
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Residues in contact with LYS 718 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714W VAL* 2.9 40.8 + - + +
715W GLN* 3.6 22.7 + - - +
717W ALA* 1.3 74.5 - - - +
719W TYR* 1.3 55.9 + - - +
721W LEU* 3.4 12.2 + - + +
722W ARG* 3.1 27.6 + - - +
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Residues in contact with TYR 719 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487W ARG* 3.6 26.0 - - + -
488W VAL 2.7 21.2 + - - -
489W CYS 4.1 0.4 - - - -
490W LEU* 3.4 35.0 - - + -
674W TYR* 3.6 8.8 - + - +
675W GLY 2.8 27.8 + - - -
676W LEU* 3.9 27.1 - - + -
715W GLN 2.8 20.6 + - - +
716W VAL* 3.4 10.3 - - - +
718W LYS* 1.3 70.5 - - - +
720W PHE* 1.3 67.9 + + - +
722W ARG* 3.2 14.0 + - + +
723W GLN* 2.9 44.4 + - + +
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Residues in contact with PHE 720 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531W VAL* 3.7 28.5 - - + -
533W ASP* 4.1 17.0 - - + -
616W ARG* 4.1 23.6 - - + -
617W ALA* 4.9 1.6 - - + -
674W TYR* 3.9 35.4 - + - -
676W LEU* 4.0 27.6 - - + -
716W VAL* 2.8 31.8 + - + +
717W ALA* 3.2 8.3 + - - +
719W TYR* 1.3 73.6 - + - +
721W LEU* 1.3 67.0 + - + +
723W GLN* 3.1 6.8 + - + +
724W MET* 2.9 50.7 + - + +
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Residues in contact with LEU 721 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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750 ASP* 5.0 16.4 - - - +
2020 SER* 4.5 13.7 - - - +
2230 LEU* 3.8 40.7 - - + +
717W ALA* 3.0 22.0 + - + +
718W LYS* 3.4 14.3 + - + +
720W PHE* 1.3 75.1 - - + +
722W ARG* 1.4 60.9 + - - +
724W MET* 3.3 17.7 + - + +
725W ALA* 3.1 24.6 + - - +
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Residues in contact with ARG 722 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
487W ARG* 3.5 47.7 + - - +
718W LYS 3.1 14.2 + - - +
719W TYR* 3.4 17.3 - - + +
721W LEU* 1.4 74.0 - - - +
723W GLN* 1.3 59.4 + - + +
725W ALA* 3.4 8.9 - - + +
726W GLN* 3.2 24.8 + - - +
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Residues in contact with GLN 723 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487W ARG* 3.0 31.2 + - - +
488W VAL* 3.5 13.3 - - - +
674W TYR* 3.2 56.7 - - + +
719W TYR* 2.9 29.1 + - + +
720W PHE* 3.4 11.9 - - + +
722W ARG* 1.3 73.8 - - + +
724W MET* 1.3 64.7 + - + +
726W GLN* 3.2 39.7 + - - +
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Residues in contact with MET 724 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2020 SER* 3.5 49.1 - - - +
2210 VAL* 3.9 39.3 - - + +
2230 LEU* 4.0 15.6 - - + +
2270 HIS* 5.3 2.1 - - - -
533W ASP* 5.4 1.8 - - - +
674W TYR* 5.8 1.3 - - - +
720W PHE* 2.9 57.5 + - + +
721W LEU* 3.3 16.5 + - + +
723W GLN* 1.3 74.4 - - + +
725W ALA* 1.4 60.3 + - - +
726W GLN 3.5 1.0 + - - -
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Residues in contact with ALA 725 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2230 LEU* 3.4 23.7 - - + +
2270 HIS* 5.6 1.8 - - - -
721W LEU 3.1 16.4 + - - +
722W ARG* 3.4 9.6 - - - +
724W MET* 1.4 74.8 - - - +
726W GLN* 1.3 66.6 + - - +
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Residues in contact with GLN 726 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487W ARG* 2.8 39.2 + - - +
488W VAL* 3.4 9.8 - - - +
722W ARG 3.2 12.1 + - - +
723W GLN* 3.2 34.2 + - - +
724W MET 3.4 0.9 - - - -
725W ALA* 1.3 80.8 - - - +
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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