Contacts of the strand formed by residues 710 - 718 (chain D) in PDB entry 1XSK
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 VAL 710 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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575D ARG* 3.7 27.6 - - - +
702D GLU* 3.4 35.7 - - + +
703D VAL 3.7 4.7 - - - +
704D PRO* 4.3 1.3 - - - -
708D GLY 5.2 0.7 - - - +
709D SER* 1.3 76.4 + - - +
711D ILE* 1.3 61.7 + - - +
712D PHE 3.7 11.4 - - - +
713D THR* 3.5 24.7 - - - +
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Residues in contact with ILE 711 (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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683D HIS* 3.7 53.2 - - + +
703D VAL 2.9 16.5 + - - +
704D PRO 3.9 13.7 - - - +
705D ALA* 4.0 20.4 - - + +
709D SER* 3.5 1.2 + - - -
710D VAL* 1.3 74.3 - - - +
712D PHE* 1.3 60.5 + - + +
729D GLY* 3.4 5.4 - - - -
730D GLU* 2.9 44.9 + - + +
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Residues in contact with PHE 712 (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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683D HIS* 4.9 1.3 - - + -
688D PHE* 3.6 33.0 - + - -
701D CYS 3.6 1.2 - - - +
702D GLU* 3.6 1.6 - - - -
703D VAL* 2.8 40.5 + - + +
710D VAL* 3.6 2.2 - - - +
711D ILE* 1.3 89.1 - - + +
713D THR* 1.3 65.2 + - - +
714D LEU* 3.8 31.6 - - + -
727D GLY* 4.2 5.2 - - - -
728D ALA 3.3 27.4 - - - -
729D GLY 3.7 14.8 - - - -
730D GLU 3.4 10.3 - - - +
731D ALA* 3.4 30.7 - - + -
734D TRP* 3.9 13.7 - + - -
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Residues in contact with THR 713 (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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700D VAL* 3.7 27.4 - - + -
701D CYS 3.4 4.5 - - - +
702D GLU* 4.1 8.7 + - + +
710D VAL* 3.5 20.1 - - - +
712D PHE* 1.3 76.3 - - - +
714D LEU* 1.3 63.3 + - - +
715D LYS* 4.2 21.5 - - + +
726D THR 4.1 0.2 - - - +
727D GLY* 3.2 3.3 - - - -
728D ALA* 2.7 46.3 + - - +
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Residues in contact with LEU 714 (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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668D LEU* 3.2 32.0 - - + +
688D PHE* 4.3 15.3 - - + -
700D VAL* 3.5 0.7 - - - -
701D CYS 2.9 35.6 + - - +
712D PHE* 3.8 26.2 - - + -
713D THR* 1.3 75.5 - - - +
715D LYS* 1.3 67.2 + - - +
716D ALA* 4.7 1.3 - - + +
725D VAL* 3.9 21.8 - - + -
726D THR 3.6 10.8 - - - +
727D GLY* 3.9 4.3 - - - -
734D TRP* 3.6 33.9 - - + -
736D LEU* 4.9 7.6 - - + -
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Residues in contact with LYS 715 (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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698D GLU* 3.0 27.5 + - + +
699D ALA 3.3 4.9 - - - +
700D VAL* 3.6 17.5 - - + +
713D THR* 4.2 20.4 - - + -
714D LEU* 1.3 82.5 - - - +
716D ALA* 1.3 61.8 + - - +
717D ALA* 4.1 0.7 - - + +
724D THR 3.5 1.4 - - - +
725D VAL* 3.3 4.0 - - - -
726D THR* 2.8 48.3 + - - +
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Residues in contact with ALA 716 (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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668D LEU* 4.4 7.4 - - + -
690D LEU* 4.0 31.2 - - + -
693D LEU* 3.2 15.5 - - + +
698D GLU* 3.5 0.8 - - - -
699D ALA 3.0 30.7 + - - +
714D LEU* 5.0 1.3 - - + -
715D LYS* 1.3 75.9 - - - +
717D ALA* 1.3 61.2 + - - +
723D ILE* 5.5 1.6 - - + -
724D THR 3.2 7.0 - - - +
725D VAL* 4.3 13.0 - - + -
736D LEU* 6.0 1.6 - - + -
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Residues in contact with ALA 717 (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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693D LEU* 4.0 0.9 - - - -
697D HIS 3.6 7.0 - - - +
698D GLU* 3.7 19.7 - - + +
715D LYS* 4.1 0.4 - - + -
716D ALA* 1.3 73.5 - - - +
718D ARG* 1.3 60.8 + - - +
719D THR* 4.0 0.7 + - - -
722D THR 3.6 1.4 - - - +
723D ILE* 3.0 3.4 - - - -
724D THR* 2.6 49.0 + - - +
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Residues in contact with ARG 718 (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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693D LEU* 3.3 28.1 + - + +
694D GLN* 3.4 17.0 - - - +
695D ASP* 3.4 32.4 - - - +
696D GLY* 3.0 26.7 + - - -
697D HIS 3.0 9.1 + - - +
717D ALA* 1.3 73.4 - - - +
719D THR* 1.3 61.8 + - - +
720D GLY 3.3 28.0 + - - +
721D ASN* 4.0 9.3 + - - -
722D THR 3.5 4.9 - - - +
723D ILE* 3.4 23.3 - - + -
772D LEU* 4.3 21.4 - - - +
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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