Contacts of the strand formed by residues 324 - 331 (chain K) in PDB entry 1IA0
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 ARG 324 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K ALA* 3.6 25.3 - - - +
80K GLU* 5.8 0.2 - - - +
81K MET* 3.6 23.5 - - + +
84K HIS* 3.5 36.2 + - + -
89K TYR* 3.6 43.9 - - + -
90K ASN 2.9 13.3 + - - +
91K VAL* 3.2 4.8 - - + -
92K CYS 2.9 22.7 + - - -
323K SER* 1.3 72.0 + - - +
325K THR* 1.3 58.2 + - - +
356K ASN* 4.5 0.2 - - - +
358K VAL* 3.8 26.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 325 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5K SER 4.4 2.4 + - - +
6K VAL* 3.4 16.8 - - + +
7K LYS* 3.1 22.0 + - - +
81K MET* 3.5 7.4 - - - +
92K CYS* 3.3 15.6 - - + +
94K PHE* 3.9 28.5 - - + -
318K ASN* 2.7 32.3 + - - +
319K LEU* 4.9 2.7 - - + -
323K SER* 3.0 17.9 + - - -
324K ARG* 1.3 70.6 - - - +
326K ALA* 1.3 66.2 + - - +
356K ASN* 3.4 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 326 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K VAL* 4.2 0.7 - - - -
7K LYS* 3.2 17.5 - - + +
77K ILE* 3.9 27.4 - - + -
81K MET* 3.5 17.3 - - + -
92K CYS 2.8 8.3 + - - +
93K ILE* 3.3 8.3 - - + +
94K PHE* 3.0 28.4 + - - -
325K THR* 1.3 81.5 - - - +
327K MET* 1.3 61.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 327 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K VAL* 4.3 3.8 - - + +
7K LYS 2.8 9.3 + - - +
8K VAL* 3.5 12.7 - - + -
9K ALA* 3.0 24.6 + - - +
77K ILE* 5.0 0.9 - - - +
94K PHE* 3.4 32.5 - - + +
96K TYR* 3.5 43.5 - - + -
282K ILE* 5.0 4.3 - - + -
326K ALA* 1.3 75.2 - - - +
328K VAL* 1.3 72.7 + - - +
329K ALA* 4.1 10.8 - - + +
347K TYR* 4.5 3.6 - - + +
348K ALA* 4.0 26.5 - - + +
351K ALA* 3.7 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 328 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K ALA* 3.2 19.7 - - + +
11K ARG* 4.8 11.4 - - + -
56K TYR* 5.6 1.1 - - + -
73K VAL* 5.2 9.2 - - + -
77K ILE* 4.9 11.0 - - + -
93K ILE* 4.3 20.4 - - + -
94K PHE 2.9 10.0 + - - +
95K ALA* 3.3 7.8 - - + +
96K TYR 2.9 23.3 + - - -
106K THR* 3.9 26.2 - - + +
107K MET* 5.5 0.9 - - - -
118K ILE* 4.5 13.9 - - + -
327K MET* 1.3 79.9 - - - +
329K ALA* 1.3 67.7 + - - +
330K ALA* 3.8 2.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 329 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9K ALA 2.7 10.0 + - - +
10K VAL* 3.1 23.7 - - + +
11K ARG 2.8 26.7 + - - -
96K TYR 3.2 6.3 - - - +
327K MET* 4.0 9.6 - - + -
328K VAL* 1.3 75.6 - - - +
330K ALA* 1.3 60.4 + - - +
331K LEU* 3.8 0.7 + - - +
344K THR* 3.7 24.2 - - + -
348K ALA* 4.0 13.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 330 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11K ARG* 3.6 8.1 - - + +
96K TYR 2.8 14.5 + - - +
97K GLY* 3.8 10.9 - - - -
98K GLN 4.3 1.0 + - - -
101K ALA* 3.4 39.1 - - + +
102K GLY 3.8 18.4 - - - +
103K LYS* 3.8 9.4 - - + +
106K THR* 5.5 2.2 - - - +
328K VAL* 3.8 4.1 + - + +
329K ALA* 1.3 71.0 - - - +
331K LEU* 1.3 66.4 + - - +
344K THR* 3.9 2.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 331 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K VAL* 3.9 18.2 - - + -
11K ARG 2.7 16.5 + - - +
12K VAL* 3.3 23.0 - - + -
13K ARG* 3.3 11.6 + - - +
28K ILE* 4.8 5.2 - - + -
30K MET* 4.3 14.6 - - + -
35K THR* 4.3 6.3 - - + -
101K ALA* 3.9 5.3 + - - +
329K ALA* 3.9 9.9 - - + +
330K ALA* 1.3 84.9 - - - +
332K SER* 1.3 67.9 + - - +
341K THR* 4.1 17.5 - - + +
344K THR* 3.6 26.5 - - + -
345K LEU* 3.7 30.5 - - + -
----------------------------------------------------------
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