Contacts of the strand formed by residues 551 - 560 (chain B) in PDB entry 1XI1
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 SER 551 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549B GLY 3.2 9.1 + - - -
550B PHE* 1.3 79.1 - - - +
552B ARG* 1.3 86.2 + - - +
571B THR* 4.0 7.5 - - - +
572B PHE 2.9 7.0 - - - -
573B THR* 2.8 30.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 552 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B ILE* 4.3 12.0 - - + +
540B GLU* 2.9 46.4 + - - +
545B ASN* 3.9 15.8 + - - +
550B PHE* 3.0 44.2 - - + +
551B SER* 1.3 87.0 + - - +
553B LYS* 1.3 63.6 + - - +
554B MET* 3.1 22.0 + - + +
571B THR* 4.2 2.8 - - - +
572B PHE* 2.9 31.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 553 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A GLU* 5.1 8.7 + - - -
552B ARG* 1.3 70.8 - - - +
554B MET* 1.3 65.7 + - - +
555B LYS 3.7 0.7 - - - -
569B ASP* 3.9 24.0 - - + +
570B ASP 4.2 2.2 - - - -
571B THR* 2.7 37.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 554 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B THR* 4.5 6.6 - - - +
536B LYS* 3.7 49.7 - - + +
537B ILE* 4.1 20.2 - - + -
540B GLU* 3.4 29.6 - - - +
552B ARG* 3.1 17.9 + - + -
553B LYS* 1.3 81.5 - - - +
555B LYS* 1.3 60.9 + - - +
556B PRO* 2.9 16.3 - - - +
569B ASP* 3.8 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 555 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B GLY* 3.5 36.7 + - - +
534B THR* 5.2 6.1 - - + -
537B ILE* 4.3 6.8 - - + +
554B MET* 1.3 77.7 - - - +
556B PRO* 1.3 71.3 - - + +
557B LYS* 3.6 7.7 + - + +
569B ASP* 4.1 0.4 - - - -
570B ASP* 2.6 48.7 + - + +
571B THR 5.5 0.7 - - - +
572B PHE* 3.9 29.1 - - + -
3D T 5.4 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 556 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
534B THR* 5.4 7.0 - - + -
536B LYS* 6.4 0.9 - - + -
554B MET 2.9 18.2 - - - +
555B LYS* 1.3 90.1 - - + +
557B LYS* 1.3 60.2 + - - +
558B PRO* 4.7 0.4 - - - +
567B LEU* 4.3 26.2 - - + -
568B VAL 2.9 11.2 - - - +
569B ASP* 3.8 10.1 - - - +
3D T 4.6 6.2 - - - +
4D T 4.5 20.6 - - + +
5D T 5.6 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 557 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A GLU* 4.4 16.0 + - - -
318A SER* 5.7 1.0 + - - -
320A GLY* 5.2 9.9 - - - -
321A GLY 5.7 1.7 - - - +
310B TYR* 5.8 0.6 + - - -
555B LYS* 4.4 11.7 - - + +
556B PRO* 1.3 76.4 - - - +
558B PRO* 1.3 85.2 - - + +
559B VAL* 3.7 7.0 - - + +
567B LEU* 3.6 3.8 - - - -
568B VAL* 2.6 33.8 + - + +
570B ASP* 4.4 25.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 558 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS* 5.1 17.0 - - - -
65B PHE* 6.0 0.4 - - + -
556B PRO 4.7 0.9 - - - +
557B LYS* 1.3 104.4 - - + +
559B VAL* 1.3 65.1 + - - +
565B VAL* 3.7 16.4 - - + -
566B VAL 3.6 7.2 - - - +
567B LEU* 3.9 14.6 - - + -
3D T 5.6 7.2 - - - +
4D T 4.6 15.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 559 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B VAL* 5.7 2.7 - - + -
557B LYS* 3.7 6.5 - - + +
558B PRO* 1.3 81.5 - - - +
560B GLN* 1.3 68.6 + - - +
561B VAL* 3.3 22.1 + - + +
565B VAL* 3.5 6.2 - - - +
566B VAL 2.9 30.3 + - - +
568B VAL* 3.6 30.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 560 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LYS 5.3 1.4 + - - -
68B ALA* 4.0 8.7 - - - +
72B ASN* 4.7 0.5 - - - +
100B TRP* 5.0 3.6 - - - -
407B LYS* 5.9 0.3 + - - -
411B ALA* 4.1 6.9 - - + +
412B LEU* 3.4 42.2 + - - +
414B PHE* 3.9 33.7 - - + -
559B VAL* 1.3 75.0 - - - +
561B VAL* 1.3 62.9 + - - +
564B GLY 3.5 9.4 - - - +
565B VAL* 3.5 23.3 - - - +
----------------------------------------------------------
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