Contacts of the strand formed by residues 94 - 103 (chain K) in PDB entry 2NX5
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 ILE 94 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K THR* 3.9 26.7 - - + -
11K ALA 3.4 4.9 - - - +
12K MET* 3.7 12.1 - - + -
78K LEU* 4.7 0.4 - - - -
92K SER 5.2 3.4 - - - +
93K HIS* 1.3 81.9 - - - +
95K ILE* 1.3 65.3 + - - +
96K GLN* 3.9 21.0 + - + +
117K ALA 3.8 0.7 - - - +
118K TYR* 3.6 6.1 - - - -
119K ASP* 3.0 33.8 + - - +
31L HIS* 4.3 12.6 - - + -
32L PRO* 3.6 29.8 - - + -
33L SER* 3.4 26.0 - - - +
34L ASP* 5.8 0.7 - - - +
62L PHE* 4.1 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 95 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11H TYR* 3.8 34.3 - - + +
9K TYR 3.9 0.7 - - - +
10K THR* 3.6 3.8 + - - -
11K ALA* 3.1 35.9 + - + +
74K TYR* 4.0 18.1 - - + +
77K SER* 4.0 28.3 - - - -
78K LEU* 4.2 16.9 - - + +
81K LEU* 3.8 28.9 - - + -
94K ILE* 1.3 72.2 - - - +
96K GLN* 1.3 67.4 + - - +
117K ALA 3.5 6.1 - - - +
118K TYR* 3.7 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K TYR 3.4 10.3 - - - +
10K THR* 4.5 1.6 - - - +
94K ILE* 3.9 13.8 - - + +
95K ILE* 1.3 80.6 - - - +
97K ARG* 1.3 61.1 + - - +
116K SER* 3.3 6.1 - - - -
117K ALA* 2.9 38.6 + - - +
120K GLY* 3.8 12.5 + - - -
31L HIS* 2.9 27.7 + - - -
56L PHE* 4.2 10.5 - - + -
60L TRP* 2.7 55.9 + - + +
62L PHE* 3.3 20.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 97 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3H LEU* 3.3 26.0 - - - +
5H GLN* 3.5 20.5 + - - +
9H THR* 4.9 9.5 + - - +
11H TYR* 3.6 23.3 + - - +
7K TYR 3.7 0.7 - - - +
8K PHE* 3.4 4.2 - - - -
9K TYR* 2.7 57.2 + - + +
74K TYR* 2.9 27.2 + - + +
96K GLN* 1.3 76.0 - - - +
98K MET* 1.3 63.1 + - - +
99K TYR* 3.9 12.6 - - + -
114K ASP* 3.2 33.4 + - - +
115K GLN 3.3 10.8 - - - +
116K SER* 3.8 4.7 - - - +
133K TRP* 5.6 1.0 - - - -
147K TRP* 5.1 7.8 - - - -
152K VAL* 5.7 2.2 - - - +
156K LEU* 3.6 10.7 - - - +
56L PHE* 3.8 1.7 - - - -
60L TRP* 4.4 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K ARG* 5.5 5.4 - - - -
7K TYR 3.3 5.6 - - - +
8K PHE* 3.8 31.9 - - + -
97K ARG* 1.3 73.9 - - - +
99K TYR* 1.3 58.8 + - - +
113K HIS* 4.5 1.6 - - - +
114K ASP* 3.5 1.3 + - - -
115K GLN* 2.8 67.0 + - + +
56L PHE* 4.3 3.8 - - - -
58L LYS* 3.2 46.4 - - + +
60L TRP* 3.5 44.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 99 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2H PRO* 3.4 7.8 - - - +
3H LEU* 3.0 29.4 + - + -
6K ARG* 3.4 10.1 - - - -
7K TYR* 3.0 54.9 + + + +
9K TYR* 2.8 42.1 + + - -
97K ARG* 3.9 23.3 - - + -
98K MET* 1.3 74.3 - - - +
100K GLY* 1.3 61.7 + - - +
113K HIS* 3.2 16.6 - - - +
114K ASP* 3.4 16.2 - - + +
156K LEU* 5.8 2.0 - - + -
159K TYR* 3.5 39.0 - + - -
160K LEU* 4.8 3.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K MET* 3.1 13.9 - - - -
6K ARG* 3.6 8.7 - - - -
99K TYR* 1.3 82.8 - - - +
101K CYS* 1.3 60.6 + - - -
112K GLY* 3.6 2.1 - - - -
113K HIS* 2.8 42.4 + - - +
160K LEU* 3.8 8.4 - - - +
164K CYS* 4.5 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K SER* 3.3 4.3 - - - -
5K MET* 3.2 28.1 + - - -
6K ARG* 4.0 0.2 - - - -
100K GLY* 1.3 73.9 - - - +
102K ASP* 1.3 64.9 + - - +
103K LEU* 5.6 0.9 - - - -
109K LEU* 3.7 20.0 - - + -
111K ARG 3.5 3.1 - - - +
160K LEU* 4.0 8.1 - - + +
164K CYS* 2.0 58.6 - - + -
165K VAL* 3.8 8.3 - - - -
168K LEU* 3.9 14.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER* 6.5 0.2 - - - -
3K HIS 3.6 4.3 - - - +
4K SER* 3.7 8.5 - - - -
6K ARG* 2.8 35.1 + - - -
101K CYS* 1.3 73.5 - - - +
103K LEU* 1.3 57.0 + - - +
109K LEU* 3.5 9.5 - - - +
110K LEU* 2.5 52.9 + - + +
111K ARG* 2.9 17.9 + - + +
113K HIS* 3.0 23.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K SER* 3.2 8.8 - - - -
3K HIS* 2.6 44.6 + - + +
101K CYS* 4.0 1.1 + - - -
102K ASP* 1.3 75.0 - - - +
104K GLY* 1.3 64.9 + - - +
107K GLY* 3.9 14.6 - - - +
108K ARG 3.4 22.4 - - - +
109K LEU* 3.7 10.1 - - + -
110K LEU* 4.2 3.3 - - - +
165K VAL* 4.3 22.0 - - + +
168K LEU* 3.7 30.5 - - + -
169K ARG* 4.7 16.4 - - + +
172K LEU* 3.9 21.3 - - + -
----------------------------------------------------------
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