Contacts of the strand formed by residues 2 - 12 (chain A) in PDB entry 2H5X
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 2 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET* 1.3 80.6 + - + +
3A ALA* 1.3 60.6 + - - +
4A SER 3.8 16.4 - - - +
5A VAL* 3.9 12.1 - - + -
26A TYR* 4.0 28.0 - - + +
48A THR* 2.9 25.3 + - - +
50A MET* 3.7 42.0 + - - +
59A LEU* 3.9 7.6 - - + -
1B MET* 4.3 14.6 - - + -
24D VAL* 4.1 19.3 - - + -
25D GLY 3.7 2.9 - - - -
26D TYR* 4.6 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 3 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A MET 3.3 1.8 + - - -
2A ILE* 1.3 70.1 - - - +
4A SER* 1.3 60.2 + - - +
47A ILE* 3.6 3.5 - - - +
48A THR* 2.8 32.6 + - - +
68A ARG* 3.5 15.7 + - - +
18D VAL* 4.4 17.9 - - + -
25D GLY 2.7 17.3 + - - +
27D ARG* 4.1 25.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 4 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 3.5 3.0 - - - +
3A ALA* 1.3 81.9 - - - +
5A VAL* 1.3 69.1 + - - +
45A ARG* 4.7 12.5 - - - -
46A LEU 3.3 16.2 - - - -
47A ILE* 4.2 8.1 - - - -
48A THR* 3.3 6.7 + - - -
10D LEU* 3.9 15.0 - - - +
18D VAL* 4.4 4.6 - - - +
20D GLU* 5.4 0.2 + - - -
23D GLY 4.4 0.4 - - - -
24D VAL* 3.6 2.3 - - - -
25D GLY* 2.8 43.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 5 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A ILE* 3.9 17.7 - - + -
4A SER* 1.3 79.8 - - - +
6A ARG* 1.3 62.2 + - - +
19A ILE* 3.8 33.0 - - + +
21A ALA* 4.4 7.6 - - + -
26A TYR* 4.0 31.2 - - + -
28A VAL* 5.7 3.1 - - + -
44A ALA 3.5 2.6 - - - +
45A ARG* 3.3 2.3 - - - -
46A LEU* 3.1 29.9 + - + -
48A THR* 4.1 14.3 - - + +
59A LEU* 4.2 14.4 - - + -
23D GLY 3.4 5.6 - - - +
24D VAL* 5.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 6 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A VAL* 1.3 74.7 - - - +
7A GLY* 1.3 62.0 + - - +
19A ILE* 3.9 2.5 - - - -
20A GLU 4.4 0.2 - - - +
21A ALA* 4.1 8.5 - - - +
43A GLU* 4.9 12.3 + - + +
44A ALA 3.1 7.6 - - - +
45A ARG* 3.5 35.9 - - + +
8D GLU* 5.1 8.9 + - - -
10D LEU* 5.7 1.2 - - - +
20D GLU* 2.7 37.2 + - - +
23D GLY* 2.7 39.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 7 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 1.3 77.0 - - - +
8A GLU* 1.3 63.8 + - - -
9A VAL 3.4 1.0 + - - -
19A ILE* 3.2 10.8 - - - +
20A GLU 3.3 13.7 - - - -
21A ALA* 5.1 0.2 - - - -
43A GLU* 3.2 18.5 - - - -
44A ALA* 2.7 36.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 8 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY* 1.3 71.2 - - - -
9A VAL* 1.3 61.1 + - - +
10A LEU* 3.0 35.2 + - + +
19A ILE* 4.3 0.7 - - - -
20A GLU* 3.0 33.5 + - + +
41A GLY* 4.1 26.1 - - - +
42A THR 3.3 9.9 - - - +
43A GLU* 3.6 14.9 + - - +
6B ARG* 5.7 3.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A GLY 4.4 0.4 - - - +
8A GLU* 1.3 68.2 - - - +
10A LEU* 1.3 59.7 + - - +
11A GLU 4.0 2.2 - - - +
12A VAL* 3.5 32.5 - - + -
17A VAL* 3.6 22.4 - - + -
18A VAL 3.6 4.9 - - - -
19A ILE* 4.6 4.9 - - + +
38A LEU* 4.6 7.9 - - + -
39A ARG 3.4 21.3 - - - +
40A GLN* 3.4 1.5 - - - -
41A GLY* 2.7 30.0 + - - -
42A THR* 2.7 18.6 + - - +
43A GLU 4.6 0.2 - - - +
44A ALA* 3.5 29.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 10 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A GLU* 3.0 41.4 + - - +
9A VAL* 1.3 74.6 - - - +
11A GLU* 1.3 60.3 + - + +
18A VAL* 2.7 27.9 + - + +
20A GLU* 3.5 38.4 - - + +
40A GLN* 3.0 23.0 + - - +
4B SER* 4.2 17.7 - - - +
6B ARG* 5.7 1.3 - - - +
45B ARG* 4.0 28.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL 3.4 1.8 + - - -
10A LEU* 1.3 84.4 - - + +
12A VAL* 1.3 71.2 + - - +
13A ALA* 4.5 6.5 - - + +
16A HIS* 4.0 13.5 - - + -
17A VAL* 3.2 9.4 - - - +
18A VAL* 3.0 50.3 + - + +
40A GLN* 4.1 9.4 - - - +
65B GLY* 6.0 2.3 - - - -
68B ARG* 4.6 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A VAL* 3.5 27.4 - - + -
11A GLU* 1.3 75.3 - - - +
13A ALA* 1.3 67.3 + - - +
14A LEU* 5.9 0.2 - - - +
16A HIS 4.1 1.8 - - - -
17A VAL* 4.5 1.6 - - + -
35A LEU* 4.1 34.1 - - + +
38A LEU* 4.0 15.9 - - + +
39A ARG* 4.3 0.2 - - - -
40A GLN* 3.8 22.7 - - + +
----------------------------------------------------------
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