Contacts of the strand formed by residues 700 - 705 (chain C) in PDB entry 4UQJ
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 TYR 700 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504C ILE* 5.0 2.0 - - - -
645C ILE* 4.5 2.5 - - - -
646C ALA* 3.2 20.6 - - + -
647C TYR* 3.8 2.2 - - - -
648C GLY* 3.6 22.3 + - - -
681C VAL* 2.8 32.9 + - + -
683C VAL* 4.1 9.5 - - + +
689C GLY* 4.0 9.6 - - - -
692C ARG* 3.5 33.2 - - + -
693C VAL* 3.5 35.6 - - + +
696C SER* 3.5 21.7 - - - +
698C GLY* 3.4 3.6 - - - -
699C LYS* 1.3 82.4 + - - +
701C ALA* 1.3 79.2 + - - +
702C TYR* 3.9 12.1 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 701 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502C ILE* 4.3 8.1 - - + -
503C MET 3.4 11.7 - - - +
504C ILE* 4.2 16.4 - - + -
633C ILE* 6.0 0.2 - - + -
639C LEU* 4.3 15.7 - - + -
645C ILE* 4.7 4.9 - - + -
646C ALA 2.8 8.2 + - - +
647C TYR* 3.1 36.2 - - + +
648C GLY 3.2 6.4 + - - -
700C TYR* 1.3 82.1 - - - +
702C TYR* 1.3 60.0 + - - +
703C LEU* 5.6 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 702 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503C MET* 2.9 44.0 + - + +
648C GLY 3.7 7.9 - - - -
649C THR 3.8 12.3 - - - -
650C LEU* 3.9 19.6 - - - +
683C VAL* 3.7 21.3 - - + -
686C THR* 3.9 31.2 + - + +
689C GLY* 4.1 17.3 - - - +
690C VAL* 4.5 1.8 - - + -
693C VAL* 3.5 21.0 - - + +
700C TYR* 3.9 13.0 - - + -
701C ALA* 1.3 75.0 - - - +
703C LEU* 1.3 78.5 + - - +
704C LEU* 3.5 41.7 - - + +
833C ZK1 6.0 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 703 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C ILE* 4.4 8.5 - - + -
501C SER 3.4 6.3 - - - +
502C ILE* 3.6 39.9 - - + -
639C LEU* 4.1 10.8 - - + -
647C TYR* 4.5 6.5 - - + -
648C GLY 3.0 12.3 + - - +
649C THR* 3.6 24.8 - - + -
650C LEU 4.6 0.5 + - - -
655C THR* 3.7 13.5 - - - +
659C PHE* 3.4 28.7 - - + -
670C MET* 3.9 16.6 - - + -
674C MET* 4.4 8.7 - - - -
702C TYR* 1.3 86.5 + - - +
704C LEU* 1.3 62.3 + - - +
727C LEU* 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 704 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500C ILE* 3.7 5.9 - - - +
501C SER* 2.8 31.8 + - - +
503C MET* 3.8 26.2 - - + -
655C THR* 4.6 8.5 - - - -
686C THR* 4.1 17.3 - - + -
690C VAL* 5.2 1.3 - - + -
702C TYR* 3.5 43.3 - - + +
703C LEU* 1.3 74.8 - - - +
705C GLU* 1.3 68.3 + - - +
708C MET* 4.4 9.0 - - + -
709C ASN* 3.8 35.2 - - + +
712C ILE* 5.2 0.7 - - + -
833C ZK1 5.3 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 705 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498C LEU* 4.2 12.8 - - + -
499C GLY 3.5 8.1 - - - +
500C ILE* 4.7 2.0 - - - +
501C SER* 3.9 0.2 - - - -
655C THR* 4.8 7.0 + - - +
704C LEU* 1.3 76.9 - - - +
706C SER* 1.3 66.2 + - - +
707C THR* 3.2 15.4 + - - +
708C MET* 3.3 2.6 + - + +
709C ASN* 3.0 19.9 + - - +
732C TYR* 4.6 0.9 - - - +
833C ZK1 4.3 25.1 - - + -
----------------------------------------------------------
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