Contacts of the strand formed by residues 639 - 646 (chain A) in PDB entry 4XUF
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 ILE 639 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
628A THR* 3.5 4.7 - - - -
629A ALA* 3.1 27.4 + - - +
632A ILE* 3.6 31.0 - - + -
633A SER* 4.6 14.1 - - - +
636A GLY* 5.1 4.3 - - - +
637A VAL* 3.2 16.6 - - + +
638A SER* 1.3 73.9 - - - +
640A GLN* 1.3 75.3 + - - +
641A VAL* 4.1 10.3 - - + -
678A LEU* 4.6 11.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 640 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
626A ASN* 3.0 25.3 - - - +
627A ALA 3.1 9.9 - - - +
628A THR* 3.9 14.7 + - - +
638A SER 5.5 1.8 + - - -
639A ILE* 1.3 84.5 - - - +
641A VAL* 1.3 64.4 + - - +
678A LEU* 5.3 0.3 - - - +
692A GLU* 5.3 0.2 - - - -
693A TYR* 3.2 40.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 641 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 5.5 1.6 - - + -
626A ASN* 3.6 6.9 - - - +
627A ALA* 3.0 53.6 + - + +
629A ALA* 3.9 27.6 - - + -
632A ILE* 5.3 1.3 - - + -
639A ILE* 4.1 9.2 - - + -
640A GLN* 1.3 80.8 - - - +
642A ALA* 1.3 61.0 + - - +
643A VAL* 4.3 4.3 - - + -
678A LEU* 3.7 25.8 - - + -
690A ILE* 3.7 20.2 - - + -
691A PHE 3.4 7.4 - - - +
693A TYR* 3.7 9.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 642 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
616A LEU* 5.4 1.1 - - + -
624A VAL* 4.6 5.4 - - + -
625A MET 3.8 5.8 - - - +
641A VAL* 1.3 73.2 - - - +
643A VAL* 1.3 60.7 + - - +
644A LYS 4.1 0.2 - - - -
689A LEU 3.1 2.9 - - - +
690A ILE* 3.4 0.4 - - - -
691A PHE* 2.5 55.0 + - + +
692A GLU 4.1 5.6 - - - +
693A TYR* 4.1 5.5 - - + +
1001A P30 3.6 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 643 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610A LEU* 4.0 17.5 - - + -
612A PHE* 3.9 8.1 - - + -
624A VAL* 3.4 7.5 - - - +
625A MET 3.0 32.3 + - - +
627A ALA* 3.6 30.7 - - + -
641A VAL* 4.3 6.5 - - + -
642A ALA* 1.3 75.9 - - - +
644A LYS* 1.3 64.0 + - - +
645A MET* 3.6 25.6 - - + +
688A TYR* 3.9 27.4 - - + -
689A LEU 3.2 5.4 - - - +
690A ILE* 4.6 5.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 644 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
623A LYS 3.9 2.5 - - - -
624A VAL* 3.5 19.3 - - + -
642A ALA 4.0 0.6 + - - -
643A VAL* 1.3 70.0 - - - +
645A MET* 1.3 65.8 + - - +
658A LEU* 3.7 19.5 - - + +
661A GLU* 3.1 30.9 + - - -
687A ILE 3.6 5.4 - - - +
688A TYR* 3.7 0.5 - - - -
689A LEU* 2.8 51.5 + - + +
691A PHE* 4.1 10.3 - - + -
831A GLY 2.6 30.2 + - - -
832A LEU* 4.3 7.4 - - - +
833A ALA* 3.7 19.1 - - - +
1001A P30 4.0 16.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 645 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612A PHE* 3.5 40.4 - - + -
622A GLY* 3.3 3.8 - - - -
623A LYS* 2.8 44.7 + - + +
625A MET* 3.7 32.8 - - + +
643A VAL* 3.6 24.9 + - + +
644A LYS* 1.3 79.1 - - - +
646A LEU* 1.3 73.2 + - - +
658A LEU* 4.5 2.5 - - - -
686A PRO* 5.9 1.1 - - + -
687A ILE 3.9 6.3 - - - +
688A TYR* 4.0 21.5 - - + -
832A LEU 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 646 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621A PHE* 3.4 14.1 - - + +
622A GLY* 4.1 5.8 - - - -
644A LYS* 6.1 0.4 - - - -
645A MET* 1.3 93.1 - - - +
647A LYS* 1.3 67.2 + - - +
648A GLU* 4.0 9.0 - - - +
654A GLU* 4.2 6.5 - - + +
655A ARG* 3.6 47.1 - - + +
658A LEU* 3.7 27.6 - - + +
686A PRO* 5.4 8.2 - - + +
687A ILE* 4.7 6.7 + - + +
832A LEU* 4.1 25.8 - - + -
----------------------------------------------------------
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