Contacts of the helix formed by residues 555 - 568 (chain A) in PDB entry 3L3N
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 555 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.3 13.0 - - - +
541A ALA* 3.4 32.6 - - - +
552A ILE* 3.0 19.9 + - - -
553A TYR 3.2 2.1 + - - -
554A GLN* 1.3 74.1 - - - +
556A LYS* 1.3 62.7 + - - +
557A GLU* 3.6 8.0 + - - -
558A ALA* 3.2 23.1 + - - +
559A GLY 3.2 15.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 556 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A THR 4.7 2.0 - - - -
325A SER* 2.7 27.7 + - - +
326A LEU 3.7 14.7 - - - +
327A GLY* 3.8 13.0 - - - +
554A GLN* 3.3 24.5 + - - +
555A SER* 1.3 70.7 - - - +
557A GLU* 1.3 78.4 + - - +
559A GLY 3.5 0.5 + - - -
560A GLN* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 557 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540A ALA* 3.8 31.1 - - + +
541A ALA* 4.9 4.0 - - - +
555A SER* 3.3 11.5 + - - +
556A LYS* 1.3 90.9 + - - +
558A ALA* 1.3 63.4 + - - +
560A GLN* 3.4 16.1 + - - +
561A ARG* 3.5 14.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 558 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 4.6 1.8 - - + -
537A LEU* 3.6 41.1 - - + +
540A ALA* 4.7 2.6 - - - +
552A ILE* 4.4 14.6 - - + -
555A SER* 3.2 26.3 + - - +
557A GLU* 1.3 73.6 - - - +
559A GLY* 1.3 67.0 + - - +
560A GLN 2.9 2.9 + - - -
561A ARG* 2.9 15.0 + - - +
562A LEU* 3.2 15.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 559 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 3.3 35.5 - - - +
327A GLY 5.9 0.2 - - - -
328A LEU* 3.3 21.3 - - - +
555A SER 3.2 8.5 + - - -
556A LYS 3.5 0.6 + - - -
557A GLU 3.5 0.2 - - - -
558A ALA* 1.3 79.3 - - - +
560A GLN* 1.3 56.6 + - - +
562A LEU* 3.6 2.0 + - - -
563A ALA* 2.9 25.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 560 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
556A LYS 3.1 17.7 + - - +
557A GLU* 3.5 9.9 - - - +
558A ALA 2.9 0.8 + - - -
559A GLY* 1.3 76.1 - - - +
561A ARG* 1.3 62.6 + - + +
563A ALA* 4.5 6.6 - - - +
564A THR* 2.8 60.9 + - - +
567A LYS* 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 561 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536A ALA* 3.8 18.6 + - - +
537A LEU* 4.2 13.5 - - + -
539A GLN* 4.0 15.2 + - - -
540A ALA* 4.0 21.7 - - - +
557A GLU 3.5 11.2 + - - +
558A ALA 2.9 6.7 + - - +
560A GLN* 1.3 74.3 - - + +
562A LEU* 1.3 67.0 + - - +
564A THR* 3.4 4.5 + - - -
565A ALA* 3.1 24.9 + - - +
580A LEU 3.9 18.6 + - - +
581A ILE* 3.1 34.4 + - - +
582A THR* 4.8 5.9 - - - +
583A GLY* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 562 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LEU* 4.4 7.6 - - + -
328A LEU* 4.2 15.7 - - + -
413A ILE* 4.2 27.4 - - + -
416A VAL* 5.1 4.0 - - + -
417A LEU* 4.1 24.7 - - + -
533A PHE* 4.9 7.9 - - + -
537A LEU* 3.8 35.4 - - + -
558A ALA 3.2 8.7 + - - +
559A GLY 4.0 5.2 - - - +
561A ARG* 1.3 80.2 - - - +
563A ALA* 1.3 56.8 + - - +
565A ALA* 3.7 3.6 - - - +
566A MET* 2.8 46.9 + - + +
581A ILE* 4.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 563 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 3.7 16.2 - - + -
393A GLN* 3.8 10.8 - - - +
559A GLY 2.9 19.8 + - - +
560A GLN* 4.0 12.3 - - - +
562A LEU* 1.3 76.9 - - - +
564A THR* 1.3 63.1 + - - +
566A MET* 3.8 1.7 - - - +
567A LYS* 2.9 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 564 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
560A GLN* 2.8 39.3 + - - +
561A ARG* 3.9 4.9 - - - -
562A LEU 3.4 0.2 - - - -
563A ALA* 1.3 75.0 - - - +
565A ALA* 1.3 63.1 + - - +
567A LYS* 3.6 15.8 + - - +
568A LEU* 3.7 14.7 + - + +
580A LEU* 3.8 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 565 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A TYR* 4.3 6.7 + - - +
409A PHE* 5.4 1.6 - - + -
561A ARG 3.1 17.2 + - - +
562A LEU 3.7 2.5 - - - +
564A THR* 1.3 75.2 - - - +
566A MET* 1.3 65.5 + - + +
568A LEU* 3.2 20.8 + - - +
569A GLY 4.1 2.3 + - - +
577A ALA* 4.0 20.6 - - + +
580A LEU* 4.1 12.7 - - + +
581A ILE* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 566 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A LEU* 4.3 9.6 - - + -
389A GLN* 3.8 20.2 - - + -
390A TYR* 3.4 57.9 - - + -
393A GLN* 3.7 22.0 - - + -
394A TYR* 3.8 8.1 + - - +
413A ILE* 3.9 33.9 - - + -
562A LEU* 2.8 47.8 + - + +
563A ALA* 3.9 4.5 - - - +
565A ALA* 1.3 73.0 - - + +
567A LYS* 1.3 61.9 + - - +
569A GLY* 3.0 13.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 567 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A LEU* 6.0 0.8 - - - +
393A GLN* 2.7 50.7 + - - +
394A TYR* 4.2 2.3 - - - +
397A LEU* 3.6 18.8 - - - +
563A ALA* 2.9 38.3 + - - +
564A THR* 3.8 9.9 - - - +
565A ALA 3.2 0.2 - - - -
566A MET* 1.3 75.2 - - - +
568A LEU* 1.3 62.5 + - + +
569A GLY 3.2 0.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 568 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
397A LEU* 3.5 3.3 - - - +
564A THR* 3.7 12.3 + - + +
565A ALA 3.2 10.7 + - - +
566A MET 3.1 1.0 - - - -
567A LYS* 1.3 79.9 - - + +
569A GLY* 1.3 68.2 + - - +
571A SER* 2.6 39.6 + - - +
572A ARG* 4.3 22.2 - - + +
576A GLU* 4.6 6.7 - - + +
577A ALA* 4.3 20.6 - - + +
580A LEU* 3.5 27.1 - - + -
----------------------------------------------------------
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