Contacts of the strand formed by residues 35 - 45 (chain C) in PDB entry 1XS2
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 HIS 35 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.6 48.5 + - + +
20C LEU 3.4 6.2 + - - -
21C PRO* 3.8 29.1 - - + +
22C LEU* 3.5 11.9 - - - +
34C THR* 1.3 117.6 + - + +
36C LYS* 1.3 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 36 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C ARG* 3.6 1.5 - - - -
20C LEU* 2.9 31.8 + - - +
22C LEU* 4.0 12.6 - - + -
35C HIS* 1.3 76.8 - - - +
37C VAL* 1.3 83.2 + - - +
38C VAL* 3.8 11.1 + - + +
53C GLU* 4.1 10.1 + - - -
54C GLY 5.1 7.0 + - - -
55C THR* 5.2 7.9 + - - +
56C MET 5.9 2.0 - - - -
298C MET* 2.9 29.9 + - - +
299C LEU* 3.2 29.0 + - + +
300C GLU* 5.2 0.8 - - - +
330C TRP* 3.8 20.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 37 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C VAL* 3.3 33.7 - - + -
18C ALA 3.3 6.1 - - - +
19C ARG* 3.6 38.8 - - + +
36C LYS* 1.3 92.8 - - - +
38C VAL* 1.3 59.2 + - - +
39C PRO* 3.4 7.8 - - - +
56C MET 5.1 1.9 - - - +
58C ALA* 5.7 7.2 - - + +
67C ILE* 3.6 27.6 - - + +
368C GLU* 4.6 5.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 38 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C VAL 3.6 2.3 - - - +
17C VAL* 3.5 3.0 - - - -
18C ALA* 2.8 37.7 + - + +
20C LEU* 4.3 23.1 - - + -
36C LYS* 4.1 20.9 - - + +
37C VAL* 1.3 77.3 - - - +
39C PRO* 1.3 60.7 - - - +
40C LEU* 3.7 22.2 + - + +
53C GLU* 3.5 36.6 - - + +
301C SER* 3.9 9.9 - - - +
330C TRP* 5.3 0.2 - - + -
334C LEU* 4.0 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 39 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C ILE* 6.0 0.2 - - + -
16C VAL 3.9 3.1 - - - +
17C VAL* 4.4 11.2 - - + -
37C VAL* 3.4 12.6 - - + +
38C VAL* 1.3 83.9 - - - +
40C LEU* 1.3 60.5 + - - +
53C GLU* 3.2 4.7 - - - -
54C GLY* 2.6 49.7 + - - +
56C MET* 4.3 11.4 - - - +
67C ILE* 4.0 29.4 - - + -
71C LEU* 4.6 13.5 - - + -
109C MET* 3.9 16.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 40 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLU 3.8 0.2 - - - +
15C ILE* 3.5 8.5 - - - +
16C VAL* 2.8 46.2 + - + +
38C VAL* 3.7 26.5 - - + +
39C PRO* 1.3 74.1 - - - +
41C LEU* 1.3 60.5 + - - +
42C ILE* 4.2 3.6 - - + -
51C VAL* 4.6 6.5 - - + -
52C ALA 3.3 5.6 - - - +
53C GLU* 3.8 17.3 - - + -
109C MET* 4.2 2.6 - - - +
301C SER* 4.6 1.1 - - - +
303C ILE* 4.3 16.4 - - + -
334C LEU* 4.2 5.6 - - + -
358C LEU* 4.1 24.9 - - + -
363C LEU* 4.0 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 41 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C ALA* 4.4 11.0 - - + -
14C GLU 3.5 13.5 - - - +
15C ILE* 4.0 17.3 - - + -
40C LEU* 1.3 73.7 - - - +
42C ILE* 1.3 62.0 + - - +
43C LEU* 4.3 17.9 - - + -
50C GLY 3.8 0.7 - - - +
51C VAL* 3.3 4.3 - - - +
52C ALA 2.9 33.8 + - - +
74C LEU* 4.4 6.5 - - + -
79C LEU* 4.1 18.6 - - + -
109C MET* 3.3 45.4 - - + +
110C VAL* 3.5 28.0 - - + +
113C ALA* 4.1 1.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 42 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C ALA 4.0 0.2 - - - +
13C ALA* 3.1 8.0 - - - +
14C GLU* 3.0 39.9 + - + +
16C VAL* 4.2 22.4 - - + -
40C LEU* 4.8 3.8 - - + -
41C LEU* 1.3 78.6 - - - +
43C LEU* 1.3 64.8 + - - +
44C HIS* 3.6 27.4 - - + +
49C GLN* 4.0 17.7 - - - +
50C GLY 3.2 8.1 - - - +
51C VAL* 4.3 11.4 - - + -
358C LEU* 3.9 23.3 - - + -
360C ARG* 3.9 20.0 - - - +
363C LEU* 5.5 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 43 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 4.1 33.9 - - + -
12C ALA 3.6 1.3 - - - -
13C ALA* 3.7 24.5 - - + -
41C LEU* 4.3 14.4 - - + -
42C ILE* 1.3 74.7 - - - +
44C HIS* 1.3 61.7 + - - +
49C GLN* 3.1 8.1 - - - +
50C GLY 2.7 37.3 + - - +
79C LEU* 4.6 1.1 - - + -
82C ILE* 4.1 15.7 - - + -
110C VAL* 3.8 16.6 - - + +
113C ALA* 3.7 26.0 - - + +
114C ALA* 3.8 13.2 - - + +
117C LEU* 3.9 10.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 44 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ILE* 3.6 5.9 - - - +
11C GLU* 2.9 27.2 + - + +
12C ALA* 2.9 39.6 + - + +
14C GLU* 2.7 35.2 + - + -
42C ILE* 3.6 13.6 - - + +
43C LEU* 1.3 75.2 - - - +
45C GLY* 1.3 59.2 + - - +
48C VAL 3.7 4.7 + - - +
49C GLN* 3.1 32.6 + - - +
117C LEU* 4.4 3.8 - - - -
360C ARG* 4.8 1.3 - - - -
372C GLU* 5.1 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 45 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C LYS 3.3 16.2 - - - -
11C GLU* 4.2 9.6 + - - -
44C HIS* 1.3 76.4 - - - +
46C GLU* 1.3 75.8 + - - +
47C GLY* 3.0 4.8 + - - +
48C VAL* 3.0 23.9 + - - +
117C LEU* 3.7 10.5 - - - +
----------------------------------------------------------
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