Contacts of the strand formed by residues 32 - 40 (chain H) in PDB entry 4NL3
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 32 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24H THR* 4.2 17.8 - - + +
25H VAL 3.3 10.3 - - - +
26H PHE* 3.6 31.3 - - + -
30H GLY 3.7 3.3 + - - +
31H PHE* 1.3 76.8 - - - +
33H LEU* 1.3 71.8 + - - +
34H ARG* 5.4 2.1 - - + +
2I LYS* 4.9 5.3 + - - +
3L GLN* 3.3 41.3 + - + +
4L GLY 4.1 17.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 33 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G THR* 4.6 4.3 - - + +
24H THR* 4.4 2.7 - - - -
25H VAL* 2.5 50.3 + - + +
27H LEU* 3.6 39.0 - - + -
32H GLN* 1.3 78.4 - - - +
34H ARG* 1.3 57.6 + - - +
35H GLY 4.0 0.2 - - - -
47H LEU* 4.9 6.7 - - + -
49H VAL* 4.2 14.4 - - + -
54H GLN* 3.5 32.1 - - + -
56H VAL* 5.0 7.2 - - + -
1L MET* 3.2 26.0 - - - +
2L LYS* 3.8 13.7 - - + +
3L GLN* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 34 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 3.5 31.0 - - + +
23H ALA 3.3 7.9 - - - +
24H THR* 4.1 20.2 + - + +
32H GLN* 5.4 2.3 - - + +
33H LEU* 1.3 72.5 - - - +
35H GLY* 1.3 58.9 + - - +
49H VAL* 3.8 24.2 - - - +
50H GLU* 5.4 1.4 + - - +
1L MET* 5.9 1.4 - - - +
3L GLN* 5.7 0.4 + - - -
74L PRO 5.2 9.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 35 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H LEU* 4.1 7.6 - - - -
23H ALA* 2.9 35.6 + - - +
25H VAL* 5.5 2.8 - - - +
33H LEU 4.0 1.6 + - - -
34H ARG* 1.3 75.5 - - - +
36H ARG* 1.3 66.0 + - - -
37H VAL* 4.4 0.7 + - - +
47H LEU* 5.1 8.0 - - - +
48H ASP 3.6 14.4 - - - -
49H VAL* 4.6 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 36 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16H LEU 5.5 0.2 - - - +
20H LYS* 2.7 53.4 + - + +
21H ILE 3.5 17.7 - - - +
22H LEU* 4.1 27.0 - - + +
35H GLY* 1.3 76.7 - - - +
37H VAL* 1.3 67.0 + - - +
38H VAL* 3.3 0.7 + - + -
47H LEU* 3.4 5.4 - - - -
48H ASP* 2.8 49.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13H LEU* 3.9 18.8 - - + +
16H LEU* 4.0 31.9 + - + -
17H ARG* 3.3 38.7 - - + +
21H ILE 4.9 1.1 + - - +
23H ALA* 5.9 2.7 - - + -
35H GLY 5.7 0.2 - - - +
36H ARG* 1.3 74.9 - - - +
38H VAL* 1.3 60.1 + - - +
39H SER 4.0 21.3 - - - +
40H PHE* 4.5 6.1 - - + -
45H VAL* 4.0 11.4 - - + -
46H LEU 3.8 3.6 - - - -
47H LEU* 3.9 13.0 - - + -
64H PHE* 4.3 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G LEU* 4.5 16.4 - - + -
17H ARG* 3.2 22.4 + - - +
36H ARG* 6.0 0.2 - - + -
37H VAL* 1.3 75.0 - - - +
39H SER* 1.3 62.5 + - - +
46H LEU* 2.7 35.4 + - + +
47H LEU 4.0 2.9 - - - +
48H ASP* 3.6 37.7 - - + +
53H GLN* 5.5 4.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 39 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 3.7 27.2 - - - +
72G LEU* 5.5 4.0 - - - -
17H ARG* 4.5 3.6 - - - +
37H VAL* 3.7 2.3 - - - +
38H VAL* 1.3 84.4 - - - +
40H PHE* 1.3 78.0 + - - +
45H VAL* 3.4 2.9 - - - +
46H LEU* 2.6 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 40 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LEU* 4.3 5.9 - - - +
10H ASP* 3.8 31.0 - - + -
13H LEU* 3.5 32.8 - - + -
14H ASN* 3.7 41.5 - - + -
17H ARG* 4.9 6.1 - - - -
37H VAL* 4.5 6.3 - - + -
39H SER* 1.3 90.2 + - - +
41H ASP* 1.3 67.8 + - - +
44H THR 3.2 14.4 - - - +
45H VAL* 4.0 15.7 - - + +
58H LYS* 4.5 2.7 - - - -
----------------------------------------------------------
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