Contacts of the strand formed by residues 555 - 560 (chain A) in PDB entry 1MS4
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 555 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550A THR 3.6 1.0 - - - +
551A MET* 3.1 5.9 - - - -
552A ALA 2.9 29.7 + - - +
553A ASN* 3.8 20.9 - - + +
554A LYS* 1.3 84.3 - - - +
556A GLY* 1.3 62.6 + - - +
557A SER* 4.2 3.4 + - - +
569A GLY* 3.6 35.4 - - - +
570A GLN 3.3 12.8 - - - +
571A THR* 4.2 9.0 - - - +
611A GLN* 4.5 5.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.7 22.0 - - - -
528A TYR* 3.6 6.6 - - - -
550A THR 2.9 9.9 - - - -
551A MET* 4.2 1.3 - - - -
555A ILE* 1.3 72.7 - - - +
557A SER* 1.3 62.8 + - - -
569A GLY* 3.1 18.2 + - - -
570A GLN 3.0 16.7 + - - +
572A VAL* 3.9 10.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 3.8 2.7 - - - +
528A TYR* 4.4 1.1 - - - -
548A VAL 3.7 0.2 - - - +
549A LEU* 3.4 4.7 - - - -
550A THR* 2.8 44.3 + - - +
555A ILE* 4.5 4.3 + - - +
556A GLY* 1.3 75.3 + - - -
558A VAL* 1.3 63.6 + - - +
559A TYR* 3.8 21.8 + - - -
564A PRO* 6.0 0.2 - - - -
568A SER* 2.7 21.5 + - - -
569A GLY* 3.5 10.9 + - - -
611A GLN* 5.4 2.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514A LEU* 4.2 12.1 - - + -
515A GLY 4.0 9.9 - - - +
516A LEU* 4.2 17.0 - - + -
526A PRO* 3.9 17.7 - - + -
528A TYR* 4.1 10.5 - - + +
547A VAL* 5.1 0.7 - - + -
548A VAL 3.3 3.6 - - - -
549A LEU* 3.8 24.0 - - + -
557A SER* 1.3 78.2 - - - +
559A TYR* 1.3 67.6 + - - +
560A ILE* 4.8 0.4 - - + -
564A PRO* 3.6 3.1 - - - +
565A LEU* 2.9 49.9 + - + +
568A SER* 3.2 5.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
546A HIS 4.2 0.7 - - - -
547A VAL* 3.4 7.1 - - - +
548A VAL* 2.7 59.2 + - + +
550A THR* 4.1 10.6 + - + -
557A SER* 3.8 28.8 + - - -
558A VAL* 1.3 77.0 - - - +
560A ILE* 1.3 66.7 + - - +
562A GLY* 4.0 15.9 - - - +
563A GLU 3.4 10.5 - - - +
564A PRO* 3.5 39.4 - - + +
611A GLN* 6.0 2.6 - - - +
614A ALA* 6.0 3.6 - - - -
617A ILE* 3.8 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
516A LEU* 3.8 28.7 - - + -
524A TRP* 3.8 26.9 - - + +
545A TYR* 3.9 27.4 - - + -
546A HIS 3.2 2.9 - - - +
547A VAL* 4.1 13.2 - - + -
558A VAL* 4.9 0.2 - - + -
559A TYR* 1.3 81.1 - - - +
561A ASP* 1.3 78.2 + - + +
562A GLY 2.8 2.9 + - - -
563A GLU* 2.9 22.5 + - - +
565A LEU* 3.7 32.3 - - + +
----------------------------------------------------------
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