Contacts of the strand formed by residues 26 - 37 (chain B) in PDB entry 3IKH
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 SER 26 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B GLY 3.9 2.4 + - - -
25B ALA* 1.3 77.4 - - - +
27B ILE* 1.3 67.9 + - - +
39D LYS* 5.2 7.8 - - - -
105D ILE* 3.3 29.7 - - - +
107D THR* 5.0 2.4 + - - -
163D SER* 5.3 3.6 - - - -
164D PRO* 3.5 33.7 - - - +
165D VAL* 4.8 7.1 + - - +
900D ATP 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B ILE* 4.3 11.0 - - + -
18B PRO* 5.0 6.3 - - + -
19B ASP 5.0 4.5 - - - +
21B PRO* 3.9 27.8 - - + -
25B ALA* 5.0 3.6 - - + -
26B SER* 1.3 83.0 + - - +
28B HIS* 1.3 79.2 + - - +
105D ILE 2.8 13.5 + - - +
106D ILE* 3.3 31.5 - - + -
107D THR* 2.8 25.8 + - - -
164D PRO* 4.8 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B PRO* 4.0 15.9 - - - +
27B ILE* 1.3 89.5 - - - +
29B GLY* 1.3 59.9 + - - +
107D THR* 3.1 21.1 - - + +
109D THR* 4.5 24.2 - - + -
137D GLY 3.6 12.3 - - - -
138D ASN* 3.0 39.7 + - - -
139D PHE 5.7 0.7 - - - -
164D PRO* 3.2 25.1 - - + +
165D VAL 5.7 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 4.8 3.1 - - - -
16B SER 3.5 10.5 - - - -
17B ILE* 3.9 10.5 - - - -
28B HIS* 1.3 75.8 - - - +
30B VAL* 1.3 68.4 + - - +
31B LYS 4.2 0.4 - - - -
106D ILE* 3.9 8.0 - - - +
107D THR 2.8 10.0 + - - -
108D THR* 3.3 22.4 + - - -
109D THR* 4.1 6.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B TRP* 3.2 5.2 - - - -
16B SER* 2.7 51.7 + - - +
29B GLY* 1.3 79.3 - - - +
31B LYS* 1.3 68.3 + - - +
32B VAL* 2.9 15.9 + - + +
108D THR* 4.8 2.0 - - - -
109D THR* 6.0 4.7 - - + -
110D ALA* 6.5 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 31 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLU* 3.0 28.2 + - - +
14B THR 3.8 6.1 - - - +
15B TRP* 4.1 33.4 - - + +
29B GLY 4.2 1.0 + - - -
30B VAL* 1.3 71.7 - - - +
32B VAL* 1.3 68.4 + - - +
33B SER* 4.5 6.5 - - - +
34B GLN* 2.7 38.2 - - - +
65B ASN* 5.4 0.6 + - - -
13D GLU* 5.9 1.2 + - - -
65D ASN* 5.9 2.6 - - - +
89D HIS* 5.4 14.5 - - + -
92D THR* 4.8 14.0 + - + +
108D THR* 4.5 13.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 32 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B THR* 2.7 29.7 + - + +
16B SER* 3.6 33.2 - - - +
30B VAL* 2.9 11.6 + - + +
31B LYS* 1.3 74.2 - - - +
33B SER* 1.3 69.0 + - - +
96B LEU* 5.7 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 33 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B ASP 4.6 0.2 - - - -
13B GLU* 3.7 3.5 - - - +
14B THR* 3.0 41.5 + - - +
31B LYS* 3.6 7.9 - - - +
32B VAL* 1.3 87.8 - - - +
34B GLN* 1.3 66.2 + - - +
35B ASP* 5.8 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 34 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.3 27.5 - - + +
12B ASP 3.6 3.1 - - - -
13B GLU* 3.7 15.3 + - + -
31B LYS* 2.7 39.1 - - - +
33B SER* 1.3 77.6 - - - +
35B ASP* 1.3 69.4 + - - +
65B ASN* 4.2 9.2 + - - +
68B TRP* 3.8 44.7 + - + +
89D HIS* 6.0 2.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.3 5.5 - - - -
12B ASP* 2.7 40.7 + - + +
33B SER* 5.9 2.5 - - - -
34B GLN* 1.3 78.9 - - - +
36B ILE* 1.3 66.8 + - - +
68B TRP* 3.8 10.8 - - - -
269B GLY* 3.7 3.3 - - - -
270B THR* 2.9 28.9 + - - +
271B LEU* 3.8 3.6 - - - +
272B SER* 2.5 45.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 36 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 4.1 15.5 - - + -
10B THR 3.4 6.7 - - - +
35B ASP* 1.3 76.2 + - - +
37B GLY* 1.3 69.0 + - - +
41B ALA* 4.1 2.5 - - + -
42B ASN* 4.0 2.6 - - - +
45B ILE* 4.0 21.1 - - + -
68B TRP* 3.9 20.4 - - + -
69B ILE* 4.0 15.0 - - + +
72B GLN* 3.4 28.5 - - + -
73B ILE* 3.9 22.0 - - + +
76B GLU* 5.9 0.2 - - + -
270B THR* 3.4 3.5 - - - +
271B LEU* 3.4 45.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B ILE* 3.9 0.3 - - - +
10B THR* 2.8 36.2 + - - -
12B ASP* 3.6 15.7 - - - -
35B ASP 3.5 1.8 + - - -
36B ILE* 1.3 74.6 - - - +
38B GLY* 1.3 64.2 + - - -
41B ALA* 3.4 15.6 - - - +
42B ASN* 3.5 9.6 - - - -
270B THR* 3.8 1.6 - - - -
----------------------------------------------------------
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