Contacts of the strand formed by residues 19 - 25 (chain D) in PDB entry 2IAM
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 MET 19 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D PRO* 4.3 8.7 - - + -
11D ARG* 3.2 62.4 - - + +
13D LEU* 3.9 12.8 - - + -
18D SER* 1.3 83.1 + - - +
20D THR* 1.3 79.1 + - - +
21D LEU* 3.4 34.3 - - + -
77D ARG* 3.5 13.7 - - - +
78D LEU* 3.3 30.8 + - + +
107D LEU* 4.2 20.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR 4.8 1.7 - - - +
8D PRO* 5.0 4.0 - - - +
19D MET* 1.3 86.7 + - - +
21D LEU* 1.3 75.5 + - - +
22D GLN* 3.3 28.8 + - - +
75D PRO* 3.9 14.6 - - + -
76D LEU 3.5 7.2 - - - +
77D ARG* 3.2 30.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D THR 3.8 15.9 - - - +
8D PRO* 4.3 4.0 - - + +
11D ARG* 5.5 0.9 - - + -
19D MET* 3.4 32.5 - - + -
20D THR* 1.3 76.5 - - - +
22D GLN* 1.3 60.1 + - - +
34D TRP* 3.8 22.4 - - + -
74D PHE 4.2 0.3 - - - +
75D PRO* 3.2 5.0 - - - +
76D LEU* 2.9 58.7 + - + +
78D LEU* 5.0 6.1 - - + -
89D TYR* 3.8 28.9 - - + -
105D SER* 4.2 17.7 - - - +
107D LEU* 5.4 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 22 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D THR 4.6 0.4 - - - +
6D GLN* 3.2 24.2 - - - +
7D THR* 3.3 27.1 + - - +
20D THR* 3.3 26.7 + - - +
21D LEU* 1.3 73.9 - - - +
23D CYS* 1.3 65.5 + - - +
24D THR* 4.7 7.4 - - - +
34D TRP* 4.1 1.8 - - - -
73D ASP* 5.0 11.1 + - - +
75D PRO* 3.6 24.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 23 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.8 11.0 - - - -
5D THR 3.6 4.7 - - - -
6D GLN* 4.4 1.3 - - + -
22D GLN* 1.3 81.2 - - - +
24D THR* 1.3 64.4 + - - +
32D MET* 3.5 14.2 - - - +
34D TRP* 3.3 15.0 - - + -
72D GLU 3.7 0.2 - - - +
73D ASP* 3.3 6.1 - - - +
74D PHE 3.0 36.1 + - - +
91D CYS* 2.0 50.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 24 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D VAL* 3.7 1.9 - - - +
5D THR* 2.9 47.2 + - - +
22D GLN* 4.7 6.2 - - - +
23D CYS* 1.3 82.5 + - - +
25D GLN* 1.3 68.8 + - - +
72D GLU* 3.2 12.8 - - + +
73D ASP* 3.2 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 25 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D GLY 4.0 8.1 - - - +
4D VAL* 4.6 5.2 - - + -
24D THR* 1.3 82.3 - - - +
26D ASP* 1.3 57.5 + - - +
27D MET* 2.9 17.2 + - + -
28D ASN* 2.7 17.4 + - - -
29D HIS* 2.6 50.9 + - - +
32D MET* 3.5 21.9 - - + -
71D THR* 3.4 16.0 + - - +
72D GLU* 3.0 24.6 + - - +
93D SER* 3.5 22.4 - - - +
----------------------------------------------------------
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