Contacts of the helix formed by residues 551 - 560 (chain N) in PDB entry 2JA7
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 PRO 551 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245N GLU* 5.1 8.5 - - - +
246N LYS* 5.8 3.6 - - - +
549N THR 4.2 4.7 - - - +
550N ASP* 1.3 93.0 - - - +
552N MET* 1.3 67.1 + - + +
554N ILE* 2.8 33.9 + - + +
555N ILE* 2.9 27.5 + - + +
582N VAL* 4.8 9.7 - - + +
583N ASN* 4.2 23.3 - - - +
628N THR* 4.7 3.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 552 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550N ASP* 3.4 27.8 + - - +
551N PRO* 1.3 79.1 - - + +
553N PRO* 1.3 61.0 - - + +
554N ILE 2.6 17.2 + - - -
555N ILE* 2.6 25.9 + - + +
556N THR* 2.6 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 553 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549N THR* 5.7 3.1 - - + -
550N ASP* 3.5 35.0 - - + +
551N PRO 3.5 1.1 - - - -
552N MET* 1.3 90.0 - - + +
554N ILE* 1.3 62.1 + - + +
556N THR* 4.9 3.8 - - - -
557N PHE* 3.2 22.3 - - - +
609N ILE* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 554 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
549N THR* 5.8 2.5 - - + -
550N ASP 4.3 8.7 - - - +
551N PRO* 2.8 10.2 + - + +
552N MET 2.6 4.8 + - - -
553N PRO* 1.3 83.6 - - + +
555N ILE* 1.3 59.3 + - - +
557N PHE* 3.9 7.5 - - + +
558N LEU* 3.2 30.1 + - + +
582N VAL* 4.8 9.2 - - + -
600N LEU* 5.6 4.0 - - + -
609N ILE* 3.5 43.7 - - + -
610N ASN 5.7 0.2 - - - +
613N VAL* 4.3 15.0 - - + -
615N MET* 6.1 0.7 - - - -
626N ILE* 4.5 26.5 - - + -
628N THR* 4.3 17.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 555 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
551N PRO* 2.9 28.5 + - + +
552N MET* 2.6 23.5 + - + +
554N ILE* 1.3 70.7 - - - +
556N THR* 1.3 71.9 + - - +
557N PHE 3.0 0.9 - - - -
558N LEU* 2.9 18.3 + - + +
559N SER* 3.2 15.6 + - - +
563N MET* 5.4 2.9 - - - +
582N VAL* 4.2 7.6 - - + -
587N HIS* 3.3 50.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 556 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552N MET* 2.6 29.7 + - - +
553N PRO* 4.9 2.9 - - - -
555N ILE* 1.3 76.9 - - - +
557N PHE* 1.3 64.6 + - - +
559N SER* 3.2 18.5 + - - -
560N GLU* 3.8 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 557 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
552N MET 4.0 1.0 + - - -
553N PRO 3.2 22.8 + - - +
554N ILE* 3.9 9.3 - - + -
555N ILE 3.0 0.2 - - - -
556N THR* 1.3 81.5 - - - +
558N LEU* 1.3 70.6 + - + +
560N GLU* 3.3 10.1 + - - +
561N TRP* 3.4 50.6 - + + -
596N LEU* 5.5 0.4 - - + -
599N THR* 4.5 5.6 - - + -
600N LEU* 3.7 23.8 - - + -
603N LEU* 3.4 49.4 - - + -
609N ILE* 5.6 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 558 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
554N ILE* 3.2 22.6 + - + +
555N ILE* 2.9 13.5 + - + +
557N PHE* 1.3 77.3 - - + +
559N SER* 1.3 53.4 + - - +
560N GLU 2.5 18.2 + - - -
561N TRP* 2.6 21.2 + - - +
562N GLY 3.6 4.5 + - - -
563N MET* 3.8 26.2 + - + +
580N VAL* 4.0 24.9 - - + -
582N VAL* 5.1 7.9 - - + -
587N HIS* 5.8 1.6 - - + -
596N LEU* 3.6 38.1 - - + -
600N LEU* 4.1 18.4 - - + -
624N LEU* 5.1 0.2 - - + -
626N ILE* 4.5 11.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 559 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
555N ILE* 3.2 9.7 + - - +
556N THR* 3.2 18.0 + - - -
558N LEU* 1.3 75.7 - - - +
560N GLU* 1.3 60.7 + - - +
561N TRP 3.4 2.6 + - - -
562N GLY 4.4 2.9 + - - -
563N MET* 3.8 32.9 + - - +
565N PRO* 5.5 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 560 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556N THR* 3.8 28.0 - - - +
557N PHE* 3.3 10.4 + - - +
558N LEU 2.5 9.7 + - - -
559N SER* 1.3 79.4 + - - +
561N TRP* 1.3 76.4 + - + -
562N GLY 3.9 0.2 - - - -
----------------------------------------------------------
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