Contacts of the strand formed by residues 652 - 660 (chain B) in PDB entry 5N4D
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 ALA 652 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
596B GLY 3.9 5.6 + - - +
597B ALA* 3.2 4.9 - - - +
598B ALA 2.9 23.6 + - - +
651B PRO* 1.3 70.2 - - - +
653B THR* 1.3 59.3 + - - +
685B HIS* 3.4 23.2 - - + +
686B PRO* 3.4 16.8 - - + +
717B PHE* 3.7 15.1 - - + -
721B ALA* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 653 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
587B ILE* 3.7 27.0 - - + +
598B ALA* 3.2 14.3 - - + +
600B PRO* 4.1 7.6 - - + -
651B PRO 2.8 19.6 + - - -
652B ALA* 1.3 72.4 + - - +
654B LEU* 1.3 61.9 + - - +
655B ILE* 3.7 27.8 - - + -
672B PHE* 5.6 0.4 - - + -
673B ILE* 5.4 0.2 - - + -
676B LEU* 4.6 5.8 - - + -
686B PRO 2.9 9.5 + - - +
687B LEU* 3.8 15.4 - - - +
688B LEU* 2.9 27.5 + - - +
717B PHE* 3.7 6.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 654 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B ALA* 4.5 6.5 - - + -
62B LEU* 4.9 11.7 - - + -
598B ALA 3.0 6.7 + - - -
599B VAL* 3.3 31.6 - - + +
600B PRO* 4.1 1.1 - - - -
653B THR* 1.3 71.6 - - - +
655B ILE* 1.3 68.4 + - - +
656B THR* 4.1 16.8 - - + -
688B LEU* 3.5 27.1 - - + +
690B LYS* 4.4 20.0 - - + +
713B ASP* 4.4 10.3 - - + +
714B LYS* 4.5 10.1 - - - -
717B PHE* 3.6 42.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 655 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
584B MET* 4.6 2.9 - - + -
600B PRO* 3.5 28.5 - - + +
602B GLY 5.5 0.2 - - - +
653B THR* 3.7 15.3 - - + -
654B LEU* 1.3 74.9 - - - +
656B THR* 1.3 65.6 + - - +
669B SER* 3.7 32.3 - - - +
672B PHE* 3.7 30.5 - - + -
673B ILE* 3.9 29.4 - - + +
688B LEU 2.9 14.6 + - - +
689B ILE* 3.3 12.3 - - + +
690B LYS* 2.8 26.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 656 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
599B VAL* 4.3 10.8 - - + -
600B PRO 3.0 6.5 + - - +
601B GLU* 3.2 26.8 - - + +
602B GLY 2.8 26.5 + - - -
654B LEU* 4.1 25.4 - - + +
655B ILE* 1.3 78.4 - - - +
657B VAL* 1.3 66.0 + - - +
658B ASN* 5.8 3.3 - - - -
690B LYS* 3.4 22.4 - - - -
714B LYS* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 657 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B GLY* 4.6 5.8 - - - +
655B ILE* 4.4 0.2 - - + -
656B THR* 1.3 79.8 - - - +
658B ASN* 1.3 70.6 + - - +
659B ILE* 4.0 13.5 - - + -
664B VAL 5.9 0.4 - - - +
666B PRO* 3.5 30.7 - - + -
669B SER* 3.5 33.9 - - - +
670B PHE* 4.5 2.9 - - + -
689B ILE* 3.9 17.0 - - + -
690B LYS 3.0 10.2 + - - +
691B ILE* 4.2 11.9 - - + -
692B ASP* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
602B GLY* 5.3 5.3 - - - -
656B THR* 4.3 3.6 + - - -
657B VAL* 1.3 83.8 - - - +
659B ILE* 1.3 63.8 + - - +
660B GLY 4.1 0.2 + - - -
663B ARG* 3.7 42.9 - - - +
664B VAL 4.9 4.9 - - - +
666B PRO* 5.6 0.5 - - - +
692B ASP* 3.7 7.0 - - + +
696B LEU* 4.3 11.3 - - + +
702B LYS* 2.9 39.7 + - - +
12D GLU* 4.0 9.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B VAL* 4.0 7.2 - - + -
658B ASN* 1.3 74.6 - - - +
660B GLY* 1.3 58.0 + - - +
663B ARG* 4.1 2.0 - - - -
666B PRO* 3.5 41.5 - - + -
670B PHE* 5.0 2.2 - - + -
691B ILE* 4.4 10.1 - - + -
692B ASP 3.3 22.0 + - - +
693B LYS* 4.2 14.4 - - + +
694B SER 3.0 21.4 + - - +
695B TRP* 3.3 39.5 - - + -
696B LEU* 3.0 13.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ARG* 4.1 7.3 + - - -
658B ASN 4.1 0.4 + - - -
659B ILE* 1.3 80.2 - - - +
661B ALA* 1.3 67.9 + - - -
662B GLY 3.5 0.5 + - - -
663B ARG* 3.3 25.4 + - - +
695B TRP* 3.8 19.6 - - - -
696B LEU 3.1 16.4 - - - -
----------------------------------------------------------
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