Contacts of the strand formed by residues 26 - 34 (chain M) in PDB entry 1I5L
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 GLU 26 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18M ILE* 4.7 10.7 - - + +
19M VAL 3.3 8.7 - - - +
20M ARG* 3.9 26.1 + - + +
24M GLY 3.6 10.7 + - - +
25M ARG* 1.3 80.7 - - - +
27M PHE* 1.3 62.9 + - - +
47M GLU* 3.5 6.1 - - - +
48M ILE* 2.6 60.6 + - + +
49M GLN* 6.2 0.2 - - - -
50M ASN* 4.9 4.9 + - - +
51M GLY* 4.9 5.2 + - - -
69M PHE* 4.6 0.5 - - - -
55N ARG* 2.7 42.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 27 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69L PHE* 3.4 38.6 - + - -
17M VAL 3.7 0.5 - - - +
18M ILE* 3.4 9.2 - - - +
19M VAL* 3.1 35.6 + - + +
21M LEU* 4.2 22.0 - - + -
25M ARG* 5.2 4.3 - - + -
26M GLU* 1.3 82.8 - - - +
28M ARG* 1.3 60.4 + - - +
42M LEU* 3.9 17.6 - - + +
45M ALA* 4.2 9.2 - - + -
46M GLU 3.2 12.8 - - - -
47M GLU* 4.5 23.1 - - + -
48M ILE* 5.0 1.6 - - - -
57M VAL* 4.6 7.4 - - + -
60M VAL* 3.9 36.3 - - + -
62M ILE* 4.6 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 28 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M PRO* 6.2 2.7 - - + -
17M VAL 3.6 4.9 - - - +
18M ILE* 3.8 31.9 - - - +
27M PHE* 1.3 75.6 - - - +
29M GLY* 1.3 59.7 + - - +
42M LEU* 4.7 0.2 - - - -
44M ASP 4.2 0.3 - - - +
45M ALA* 3.1 7.6 - - - +
46M GLU* 3.0 46.8 + - + +
48M ILE* 3.6 31.7 - - + +
51M GLY* 5.1 8.7 - - - -
73M ALA* 4.3 18.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16M PRO* 3.1 6.9 - - - +
17M VAL* 2.6 42.2 + - - +
27M PHE 4.0 0.4 - - - -
28M ARG* 1.3 78.5 - - - +
30M THR* 1.3 62.6 + - - -
42M LEU* 4.2 11.3 - - - +
44M ASP 4.1 10.8 - - - -
45M ALA* 4.2 6.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 30 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14M LYS* 3.7 33.2 - - - +
15M SER 3.4 7.3 - - - +
16M PRO* 4.9 3.5 - - - +
29M GLY* 1.3 73.6 - - - -
31M LEU* 1.3 63.4 + - - +
32M ASP* 3.0 9.1 + - - +
42M LEU* 3.1 6.2 - - - -
43M LEU* 3.0 51.5 + - + +
44M ASP* 4.9 3.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 31 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9M LEU* 3.5 47.6 - - + +
12M SER* 3.6 23.6 - - - +
13M LEU* 3.3 12.7 - - + +
14M LYS 2.8 23.5 + - - -
15M SER 3.0 11.4 + - - +
17M VAL* 4.0 17.5 - - + +
29M GLY 3.9 2.0 + - - -
30M THR* 1.3 67.2 - - - +
32M ASP* 1.3 57.3 + - - +
33M GLY 3.5 23.6 - - - +
34M TYR* 4.8 3.1 - - + -
40M LEU* 4.6 16.6 - - + -
41M VAL 3.8 7.2 - - - +
42M LEU* 3.9 10.1 - - + -
70M VAL* 5.2 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 3.2 32.2 - - - +
8L VAL* 4.8 7.3 - - - +
11L ARG* 4.8 6.4 + - - -
13M LEU* 3.5 7.4 - - - +
14M LYS* 4.9 11.1 - - - +
30M THR* 3.0 6.3 + - - +
31M LEU* 1.3 73.7 - - - +
33M GLY* 1.3 58.5 + - - +
41M VAL* 3.1 19.6 + - + +
43M LEU* 3.2 46.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 33 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 3.9 14.6 - - - -
4L ARG 4.3 1.1 - - - -
13M LEU* 4.1 5.4 - - - +
31M LEU* 3.5 10.9 - - - +
32M ASP* 1.3 80.8 - - - +
34M TYR* 1.3 69.9 + - - +
40M LEU* 3.7 0.9 - - - -
41M VAL* 3.2 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 34 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3L PRO* 4.5 10.1 - - + +
4L ARG* 4.2 6.4 + - - +
5L PRO* 3.6 14.9 - - - +
6M LEU* 4.1 24.1 + - + -
9M LEU* 4.2 13.9 - - + -
10M ASN* 2.6 60.7 + - + +
13M LEU* 4.0 21.3 - - + -
31M LEU* 4.8 5.2 - - + -
33M GLY* 1.3 80.2 - - - +
35M ASP* 1.3 71.9 + - - +
38M MET* 5.4 0.4 - - - -
39M ASN 3.2 13.9 - - - +
40M LEU* 3.7 13.9 - - + -
----------------------------------------------------------
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