Contacts of the helix formed by residues 663 - 673 (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 GLN 663 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A ALA* 3.4 24.5 - - - +
93A ASP* 3.5 19.0 - - + +
94A THR* 3.1 25.7 + - - +
97A ASP* 3.1 20.6 + - - -
652D PRO 3.9 6.3 + - - -
662D HIS* 1.3 97.2 - - + +
664D SER* 1.3 65.8 + - - +
665D LEU* 3.3 2.4 + - - +
666D ALA* 3.1 16.1 + - + +
667D ILE* 3.0 19.3 + - - +
3800D GSH 3.1 34.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 664 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
614D ARG* 3.1 35.0 + - - +
617D ILE* 4.5 3.3 - - - +
618D ILE* 3.9 11.0 - - - +
652D PRO* 3.7 19.2 - - - +
663D GLN* 1.3 71.9 - - - +
665D LEU* 1.3 69.2 + - - +
667D ILE* 3.4 2.4 + - - +
668D ALA* 2.9 28.2 + - - +
752D TYR* 5.2 0.9 + - - -
3800D GSH 2.5 31.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 665 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93A ASP* 4.1 15.5 - - - +
617D ILE* 4.7 4.5 - - + -
663D GLN* 3.3 1.6 + - - +
664D SER* 1.3 89.7 + - - +
666D ALA* 1.3 67.1 + - - +
668D ALA* 3.7 3.9 - - - +
669D ARG* 3.0 35.3 + - - +
692D VAL* 3.5 33.0 - - + -
693D ASP* 3.6 17.7 - - - +
696D ASP* 3.7 28.3 - - + +
748D TRP* 3.8 16.2 - - + -
752D TYR* 3.9 25.1 - - + +
3800D GSH 4.6 1.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 666 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS* 3.5 13.8 - - - +
89A ASP* 3.7 12.0 - - + +
90A ALA 3.6 27.1 - - - +
93A ASP* 4.5 3.1 + - - +
662D HIS 3.7 9.6 - - - +
663D GLN* 3.1 16.7 + - + +
665D LEU* 1.3 79.0 - - - +
667D ILE* 1.3 62.5 + - - +
669D ARG* 3.5 14.4 + - - +
670D TYR* 3.1 22.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 667 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS* 4.1 6.1 - - - -
618D ILE* 3.6 27.6 - - + -
652D PRO 4.2 8.1 - - - +
653D ILE 4.2 1.1 - - - -
654D LEU* 3.4 43.3 - - + +
661D LEU* 3.8 35.0 - - + +
662D HIS* 3.7 14.1 - - - +
663D GLN 3.0 20.9 + - - +
664D SER 3.6 6.1 - - - +
666D ALA* 1.3 74.3 - - - +
668D ALA* 1.3 64.9 + - - +
670D TYR* 3.0 4.8 + - + +
671D LEU* 3.0 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 668 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
617D ILE* 4.1 12.1 - - + -
618D ILE* 4.3 5.6 - - + +
621D ILE* 3.6 22.6 - - + +
664D SER 2.9 18.7 + - - +
665D LEU* 3.7 2.0 - - - +
667D ILE* 1.3 75.5 - - - +
669D ARG* 1.3 62.1 + - - +
671D LEU* 3.3 4.2 + - - +
672D THR* 3.1 28.9 + - - +
748D TRP* 3.5 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 669 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 3.5 46.6 - - - +
73A LYS* 5.8 1.8 - - - +
89A ASP* 3.1 28.9 + - - +
93A ASP* 5.4 3.2 + - - -
665D LEU* 3.0 27.7 + - - +
666D ALA* 3.7 6.3 - - - +
668D ALA* 1.3 76.4 - - - +
670D TYR* 1.3 63.1 + - - +
672D THR* 3.0 21.0 + - - +
673D LYS* 3.1 28.8 + - + +
689D ASP* 2.8 35.6 + - - +
692D VAL* 5.3 1.2 - - - +
693D ASP* 4.8 10.1 + - - -
748D TRP* 4.0 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 670 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A GLU* 3.6 37.1 - - + +
83A MET* 3.4 40.3 - - + +
86A CYS* 3.9 19.1 - - + -
602D PRO* 6.0 0.9 - - - +
604D TYR* 4.5 14.9 + + - -
654D LEU* 5.0 0.9 - - + -
656D VAL* 4.1 11.1 - - + +
661D LEU* 4.0 19.1 - - + -
666D ALA 3.1 13.6 + - - +
667D ILE 3.0 7.5 + - - +
669D ARG* 1.3 76.7 - - - +
671D LEU* 1.3 86.2 + - + +
673D LYS* 3.3 28.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 671 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D TYR* 3.9 32.8 - - + +
618D ILE* 3.8 23.1 - - + +
621D ILE* 3.8 20.9 - - + -
622D PHE* 3.7 33.2 - - + -
625D LEU* 3.5 20.0 - - + +
627D ILE* 5.4 5.3 - - + +
654D LEU* 4.2 2.0 - - + -
667D ILE* 3.0 24.5 + - + +
668D ALA* 3.7 7.0 - - - +
670D TYR* 1.3 88.9 - - + +
672D THR* 1.3 60.6 + - - +
673D LYS 3.8 1.6 + - - +
675D THR* 4.0 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 672 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621D ILE* 3.6 28.3 - - + -
668D ALA 3.3 13.6 + - - +
669D ARG* 3.0 17.9 + - - +
671D LEU* 1.3 77.2 - - - +
673D LYS* 1.3 65.8 + - - +
674D ASN 3.3 0.3 + - - -
675D THR* 2.6 31.1 + - - -
677D LEU* 3.9 13.0 - - + -
678D ALA* 3.4 23.1 - - - +
748D TRP* 3.6 25.3 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 673 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A ARG* 5.9 1.4 - - - +
73A LYS* 6.1 6.6 - - - +
82A GLU* 3.9 31.3 + - + +
85A GLN* 2.9 40.0 + - - +
86A CYS* 5.6 0.8 - - - +
89A ASP* 4.8 4.4 + - - -
669D ARG* 3.1 35.7 + - + +
670D TYR* 3.3 20.9 + - - +
671D LEU 3.4 1.9 - - - +
672D THR* 1.3 78.5 - - - +
674D ASN* 1.3 74.3 + - - +
675D THR* 3.3 6.8 + - - +
678D ALA* 4.7 5.2 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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