Contacts of the helix formed by residues 399 - 407 (chain I) in PDB entry 4XLN
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 ASN 399 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I ASP 3.9 3.6 - - - +
397I GLU* 2.8 7.2 + - - -
398I THR* 1.3 75.9 - - - +
400I PRO* 1.3 74.7 - - + +
401I LEU* 2.9 19.2 + - - +
402I SER* 2.7 48.2 + - - -
403I SER* 3.5 4.7 + - - -
565I GLN 3.6 13.3 + - - +
566I THR 3.3 10.7 + - - -
568I ALA* 3.2 28.3 + - + +
569I VAL 5.5 0.2 - - - -
570I PRO* 4.9 9.4 - - + -
659I PRO* 5.8 0.2 - - - -
660I ALA* 4.5 11.1 - - + +
668I LEU* 5.2 4.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 400 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ASN* 1.3 88.7 - - + +
401I LEU* 1.3 57.9 + - - +
403I SER* 2.8 25.0 + - - +
404I LEU* 2.9 15.4 + - - +
587I VAL* 6.0 0.7 - - + -
588I VAL* 5.5 4.7 - - + -
591I SER* 3.7 28.7 - - - +
593I ALA* 3.9 17.0 - - + -
637I PHE* 5.7 3.4 - - + -
658I GLY* 6.2 0.2 - - - -
659I PRO* 4.6 13.0 - - + -
660I ALA* 3.7 34.3 - - + +
661I SER* 6.2 0.7 - - - -
666I LEU* 4.4 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 401 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
399I ASN* 2.9 9.5 + - - +
400I PRO* 1.3 77.8 - - - +
402I SER* 1.3 59.1 - - - +
404I LEU* 3.7 15.5 - - + -
405I ARG* 2.9 28.8 + - - +
542I LEU* 4.5 17.7 - - + -
543I ASN* 3.6 19.5 + - - +
546I LEU* 3.6 35.0 - - + -
565I GLN* 3.6 26.2 - - + +
587I VAL* 3.7 18.3 - - + +
666I LEU* 3.7 20.6 - - + +
668I LEU* 4.7 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 402 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I ASP* 3.0 34.6 - - - +
398I THR* 3.3 3.5 + - - -
399I ASN* 2.7 40.8 + - - +
401I LEU* 1.3 77.6 - - - +
403I SER* 1.3 58.0 + - - +
405I ARG* 3.9 1.9 - - - +
406I HIS* 2.9 28.8 + - - +
566I THR* 3.2 29.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 403 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124I ASP* 5.4 0.5 + - - -
395I LYS* 3.3 34.4 + - - -
396I ASP* 3.0 23.1 + - - +
399I ASN 3.5 1.8 + - - -
400I PRO* 2.8 24.5 + - - +
402I SER* 1.3 72.4 - - - +
404I LEU* 1.3 66.5 + - - +
406I HIS* 3.0 7.8 + - - +
407I LYS* 2.9 37.5 + - - +
591I SER* 5.5 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 404 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I LEU* 3.9 22.2 - - + -
19I THR* 4.1 11.9 - - + -
400I PRO 2.9 18.0 + - - +
401I LEU* 3.7 7.4 - - + +
403I SER* 1.3 79.2 + - - +
405I ARG* 1.3 59.1 + - - +
407I LYS* 4.0 7.3 + - - +
408I ARG* 3.4 23.7 + - - +
542I LEU* 3.7 22.9 - - + -
587I VAL* 3.6 43.5 - - + +
590I ASP* 3.7 26.7 - - + +
591I SER* 4.1 7.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 405 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396I ASP* 4.3 6.7 + - - -
401I LEU* 2.9 18.1 + - + +
402I SER 4.0 1.1 - - - +
404I LEU* 1.3 73.4 - - - +
406I HIS* 1.3 67.7 - - - +
407I LYS 3.1 2.5 - - - -
408I ARG* 2.9 24.7 + - + +
409I ARG* 3.0 58.5 + - + +
442I GLU* 3.4 20.2 + - - +
454I SER* 4.1 5.8 - - - +
541I SER* 6.1 0.4 - - - -
542I LEU* 4.7 6.9 - - + +
543I ASN* 3.1 36.8 - - - +
563I ASN* 3.5 12.1 + - - +
566I THR* 2.7 43.5 + - - +
2T C 5.0 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 406 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135I VAL* 3.5 17.9 - - + +
137I VAL* 3.9 18.6 - - + +
393I GLN* 3.4 23.3 + - + -
394I PHE 3.2 26.2 - - - -
395I LYS* 5.1 0.6 - - + +
396I ASP* 3.3 32.0 + - + +
402I SER 2.9 20.3 + - - +
403I SER* 3.0 9.4 + - - +
405I ARG* 1.3 88.8 - - - +
407I LYS* 1.3 62.2 + - + +
408I ARG 3.5 0.2 + - - -
409I ARG* 3.6 18.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 407 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I LEU 6.0 0.2 - - - +
19I THR* 4.5 13.2 - - + -
21I ILE* 4.2 5.5 - - + +
22I GLN* 3.4 37.8 + - + +
124I ASP* 3.2 28.3 - - - +
125I GLY 3.2 20.0 + - - +
126I SER* 3.3 22.0 - - - -
135I VAL* 3.7 21.9 - - + +
136I ILE 5.1 1.9 - - - +
137I VAL* 5.8 1.1 - - - +
138I SER* 4.6 4.7 + - - -
395I LYS* 3.5 20.4 - - + +
403I SER* 2.9 27.4 + - - +
404I LEU* 4.2 7.9 - - - +
406I HIS* 1.3 76.6 - - + +
408I ARG* 1.3 61.7 + - + +
409I ARG 3.3 4.5 + - - +
----------------------------------------------------------
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