Contacts of the helix formed by residues 65 - 75 (chain B) in PDB entry 2XFN
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 GLN 65 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B TYR 4.1 1.4 + - - +
61B VAL* 3.1 18.6 - - - +
62B GLY 3.1 33.8 + - - +
64B THR* 1.3 75.3 - - - +
66B ASN* 1.3 61.8 + - - +
68B ILE* 3.5 5.7 - - + +
69B LEU* 3.2 25.0 + - + +
205B GLY* 4.1 11.9 + - - -
432B TRP* 3.3 55.9 - - + +
435B TYR* 3.8 13.8 - - - -
437B GLU* 3.0 33.1 + - + +
1500B FAD 5.0 1.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR* 3.3 27.5 + - - +
65B GLN* 1.3 75.7 - - - +
67B ARG* 1.3 60.2 + - - +
69B LEU* 3.8 5.2 - - - +
70B ARG* 2.9 30.1 + - - +
437B GLU* 3.3 2.8 + - - -
466B GLU* 3.6 19.7 + - + +
467B PRO 3.5 16.0 + - - +
468B GLU* 3.6 21.4 + - - +
469B SER* 2.9 35.8 + - - +
472B VAL 4.7 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN* 1.3 75.2 - - - +
68B ILE* 1.3 61.7 + - - +
70B ARG* 3.3 13.0 + - - +
71B LEU* 2.9 30.7 + - - +
431B HIS* 4.5 14.8 + - - +
437B GLU* 3.0 21.1 + - - +
440B VAL* 3.8 19.5 - - + +
441B GLU* 3.7 48.9 + - - +
444B GLU* 5.1 2.6 + - - -
448B ARG* 6.0 1.6 - - - +
464B GLN 2.9 27.9 + - - -
465B SER* 4.0 3.0 - - - +
466B GLU* 3.7 41.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.3 9.9 - - + -
61B VAL* 4.0 17.5 - - + -
65B GLN* 3.5 18.4 - - + +
67B ARG* 1.3 74.2 - - - +
69B LEU* 1.3 59.7 + - - +
71B LEU* 4.5 2.7 - - + -
72B ALA* 2.9 29.5 + - - +
210B PHE* 4.1 17.0 - - + -
217B VAL* 4.3 25.4 - - + -
436B MET* 4.1 21.1 - - + -
437B GLU* 2.9 38.7 + - + +
440B VAL* 3.8 22.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B VAL* 3.8 29.4 - - + -
62B GLY 4.0 15.0 - - - +
63B PRO* 5.3 0.2 - - + -
65B GLN 3.2 22.1 + - - +
66B ASN* 3.8 6.1 - - - +
67B ARG 3.2 0.4 - - - -
68B ILE* 1.3 80.7 - - + +
70B ARG* 1.3 57.4 + - - +
72B ALA* 3.9 3.3 - - - +
73B LYS* 2.9 31.1 + - - +
79B THR* 4.1 11.7 - - + -
210B PHE* 4.6 3.3 - - + -
469B SER* 3.8 22.4 - - - +
472B VAL* 3.6 41.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 70 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B ASN 2.9 18.1 + - - +
67B ARG* 3.7 20.7 - - - +
69B LEU* 1.3 74.3 - - - +
71B LEU* 1.3 84.1 + - - +
73B LYS* 3.3 7.2 + - - +
74B GLU* 3.0 35.1 + - + +
440B VAL* 4.5 0.2 - - - +
444B GLU* 2.8 43.4 + - - -
466B GLU* 2.9 41.9 + - - +
467B PRO 6.0 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 4.8 1.3 - - + -
18B ALA* 4.2 14.1 - - + -
21B LYS* 4.0 32.5 - - + +
67B ARG 2.9 17.6 + - - +
68B ILE* 3.9 4.5 - - + +
70B ARG* 1.3 95.9 - - - +
72B ALA* 1.3 62.6 + - - +
74B GLU* 3.2 9.4 + - + +
75B LEU* 3.1 40.2 + - + +
217B VAL* 4.0 13.0 - - + -
221B ILE* 4.0 18.2 - - + -
440B VAL* 3.8 25.4 - - + -
444B GLU* 4.9 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B ILE* 2.9 17.1 + - - +
69B LEU 3.9 2.2 - - - +
71B LEU* 1.3 77.5 - - - +
73B LYS* 1.3 63.6 + - - +
75B LEU* 3.2 8.7 + - - -
76B GLY 3.2 5.7 + - - -
77B LEU* 3.0 41.5 + - + +
210B PHE* 3.3 36.6 - - + -
217B VAL* 4.3 5.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B LEU 2.9 20.2 + - - +
70B ARG* 3.6 7.9 - - - +
71B LEU 3.2 0.2 - - - -
72B ALA* 1.3 75.6 - - - +
74B GLU* 1.3 59.3 + - - +
76B GLY* 3.0 19.9 + - - -
77B LEU 3.9 14.1 - - - +
470B VAL* 3.9 14.3 - - - +
471B ASP* 2.9 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 2.7 38.7 + - - -
25B ASP* 4.7 0.2 - - - +
70B ARG* 3.0 31.0 + - + +
71B LEU* 3.6 8.7 - - + +
73B LYS* 1.3 77.5 - - - +
75B LEU* 1.3 61.7 + - + +
76B GLY* 3.4 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 75 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B LYS* 4.4 9.6 - - - -
71B LEU* 3.1 24.1 + - + +
72B ALA* 3.2 9.8 + - - +
74B GLU* 1.3 76.1 - - + +
76B GLY* 1.3 57.7 + - - +
77B LEU* 3.5 3.4 - - + -
217B VAL* 3.6 42.2 - - + +
220B ARG* 2.9 42.7 + - + +
221B ILE* 3.8 23.6 - - + -
224B LEU* 4.0 22.2 - - + -
----------------------------------------------------------
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