Contacts of the strand formed by residues 622 - 630 (chain B) 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 GLY 622 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
618B SER* 3.3 4.4 + - - -
619B GLY* 2.5 34.3 + - - -
620B ALA 3.8 0.4 - - - -
621B PHE* 1.3 81.1 - - - +
623B LYS* 1.3 55.8 + - - -
645B MET 3.4 12.1 - - - -
646B LEU* 4.1 5.8 - - - -
647B LYS* 3.9 6.9 - - - +
832B LEU* 3.1 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 623 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B VAL* 4.5 10.2 - - + +
617B GLY 3.8 5.2 - - - -
618B SER* 3.5 18.8 - - - +
619B GLY 4.4 0.2 - - - +
622B GLY* 1.3 73.2 - - - -
624B VAL* 1.3 66.8 + - - +
625B MET* 3.7 30.2 - - + -
643B VAL 3.9 0.5 - - - +
644B LYS* 4.3 1.1 - - - +
645B MET* 2.9 54.2 + - + +
646B LEU 5.2 0.2 - - - -
647B LYS* 3.9 37.9 - - - +
832B LEU 3.9 0.6 + - - -
833B ALA* 4.9 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 624 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
615B VAL* 3.6 2.8 - - - +
616B LEU* 2.8 31.4 + - + -
617B GLY 3.0 15.9 + - - +
623B LYS* 1.3 76.3 - - - +
625B MET* 1.3 70.0 + - - +
642B ALA* 4.3 11.2 - - + -
643B VAL 3.4 9.0 - - - +
644B LYS* 4.0 19.7 - - + -
830B PHE* 5.5 1.6 - - + -
833B ALA* 3.5 27.4 - - + -
1001B P30 3.9 39.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 625 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B PHE* 4.1 27.6 - - + -
613B GLY 3.5 23.1 - - - +
614B LYS 3.7 5.2 - - - +
615B VAL* 3.7 25.6 - - + -
616B LEU* 4.1 5.2 - - - +
623B LYS* 3.7 29.2 - - + -
624B VAL* 1.3 78.6 - - - +
626B ASN* 1.3 65.3 + - - +
642B ALA* 3.5 5.0 - - - -
643B VAL* 2.9 32.5 + - + +
645B MET* 3.9 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 626 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
612B PHE* 3.6 1.2 - - - -
613B GLY* 2.6 33.0 + - - -
614B LYS* 2.8 41.5 + - + +
616B LEU* 3.8 15.3 - - + +
625B MET* 1.3 75.4 - - - +
627B ALA* 1.3 85.9 + - - +
640B GLN* 3.3 16.2 + - - +
641B VAL 3.4 9.5 + - - +
693B TYR* 3.2 35.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 627 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
610B LEU* 4.5 7.2 - - + -
611B GLU 3.2 12.6 - - - +
612B PHE* 3.9 12.6 - - + -
613B GLY* 4.2 0.7 - - - +
626B ASN* 1.3 87.7 + - - +
628B THR* 1.3 63.6 + - - +
640B GLN* 3.4 3.7 - - - +
641B VAL* 2.9 36.8 + - + +
643B VAL* 3.7 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 628 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B ASN 3.6 3.5 - - - +
610B LEU* 4.6 0.4 - - - -
611B GLU* 2.6 54.7 + - - +
627B ALA* 1.3 73.5 - - - +
629B ALA* 1.3 61.6 + - - +
630B TYR* 3.9 17.8 + - + +
638B SER* 4.0 24.5 - - - +
639B ILE 3.6 10.5 - - - +
640B GLN* 3.6 19.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 629 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B PHE* 4.4 2.7 - - + -
609B ASN 3.3 5.4 - - - +
610B LEU* 3.6 22.2 - - + -
627B ALA 4.0 0.6 - - - -
628B THR* 1.3 73.7 - - - +
630B TYR* 1.3 61.7 + - - +
631B GLY 3.7 1.0 + - - -
632B ILE* 3.8 32.6 - - + +
637B VAL 4.0 0.9 - - - +
638B SER* 3.4 3.4 - - - -
639B ILE 3.2 28.3 + - - -
641B VAL* 3.9 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 630 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B PHE* 3.4 15.8 - - - -
609B ASN* 2.8 50.3 + - + +
611B GLU* 3.2 29.1 + - + -
628B THR* 3.9 19.5 - - + +
629B ALA* 1.3 70.1 - - - +
631B GLY* 1.3 62.5 + - - +
632B ILE 3.2 1.3 - - - -
636B GLY 5.6 2.9 - - - +
637B VAL 5.5 0.2 - - - -
638B SER* 3.2 34.0 + - - +
----------------------------------------------------------
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