Contacts of the strand formed by residues 25 - 32 (chain A) in PDB entry 1YQS
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 GLY 25 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A LEU* 4.0 4.3 - - - -
23A ALA* 3.7 5.2 - - - +
24A PRO* 1.3 75.6 - - - +
26A ALA* 1.3 64.3 + - - +
41A GLU 3.3 11.2 - - - -
43A VAL 3.6 11.0 - - - -
52A ILE* 4.0 10.3 - - - -
323A ALA* 3.4 2.1 - - - -
324A ASN* 2.8 34.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.7 20.8 - - + +
18A ALA* 4.1 9.0 - - + -
19A LEU* 3.9 15.0 - - + -
23A ALA* 4.7 0.4 - - + -
25A GLY* 1.3 75.6 - - - +
27A MET* 1.3 62.7 + - - +
40A SER* 3.4 0.9 - - - -
41A GLU 2.9 31.6 + - - +
52A ILE* 4.0 3.7 - - - +
322A LEU 3.3 11.0 - - - +
323A ALA* 4.3 2.0 - - + -
335A MET* 4.1 15.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.8 5.5 - - - +
26A ALA* 1.3 77.8 - - - +
28A VAL* 1.3 63.8 + - - +
39A LEU 3.2 13.9 - - - +
40A SER* 3.6 9.9 - - - +
52A ILE* 4.0 14.4 - - + -
53A THR 3.0 34.8 - - - +
54A THR* 3.5 9.6 - - + -
56A ASP* 3.8 23.1 - - + +
58A PHE* 4.1 10.3 - - + -
210A ALA* 5.4 0.7 - - + -
244A THR* 4.2 13.7 - - + -
320A THR 4.7 0.2 - - - -
321A ALA* 3.2 4.5 - - - +
322A LEU* 2.8 63.1 + - + +
335A MET* 4.1 2.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A LEU* 4.1 31.4 - - + -
15A LEU* 4.3 10.1 - - + -
27A MET* 1.3 77.7 - - - +
29A ARG* 1.3 66.6 + - - +
30A VAL* 4.6 4.3 - - + -
37A HIS 4.5 0.2 - - - -
38A GLN* 3.4 2.9 - - - -
39A LEU* 2.9 51.5 + - + +
54A THR* 3.6 4.9 - - - +
244A THR* 5.0 0.4 - - - -
319A VAL* 3.7 24.2 - - + -
320A THR 3.3 12.6 - - - +
321A ALA* 4.0 10.3 - - + -
338A THR* 4.2 12.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28A VAL* 1.3 75.8 - - - +
30A VAL* 1.3 65.2 + - - +
31A ASP* 3.0 34.2 + - - +
36A ILE* 3.6 30.2 - - + +
37A HIS 3.2 10.3 - - - +
38A GLN* 4.5 11.6 + - + +
54A THR* 4.7 10.0 + - + -
55A THR* 6.2 3.0 - - - +
244A THR* 3.4 30.0 - - - +
245A GLN* 3.8 50.3 + - - +
248A ASP* 3.2 8.2 - - - +
319A VAL* 3.4 1.7 - - - +
320A THR 2.9 30.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PRO* 4.3 9.9 - - + -
11A LEU* 4.1 14.6 - - + -
28A VAL* 4.6 2.7 - - + -
29A ARG* 1.3 76.4 - - - +
31A ASP* 1.3 67.3 + - - +
32A ASP* 4.1 8.1 - - + +
35A THR 3.7 0.2 - - - +
36A ILE* 3.4 7.6 - - - +
37A HIS* 2.8 50.9 + - + +
317A ARG* 3.9 21.8 - - + -
318A SER 3.3 10.5 - - - +
319A VAL* 3.9 14.4 - - + -
342A ALA* 3.8 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 31 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ARG* 3.0 24.5 + - - -
30A VAL* 1.3 70.5 - - - +
32A ASP* 1.3 59.8 + - - +
33A ASN 3.5 3.1 + - - -
34A GLY 4.8 3.1 - - - +
35A THR 3.9 2.9 - - - -
36A ILE* 2.7 30.7 - - + +
245A GLN* 4.7 1.4 - - - +
248A ASP* 2.5 33.9 - - + +
316A LYS 3.5 1.6 - - - +
317A ARG* 3.2 6.1 - - - +
318A SER* 2.9 42.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 32 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 5.3 0.5 - - - +
5A ALA* 5.3 0.3 - - - -
6A PRO* 3.5 16.3 - - + +
30A VAL* 3.7 9.4 - - + -
31A ASP* 1.3 69.6 - - - +
33A ASN* 1.3 73.6 + - - +
34A GLY 3.2 0.7 - - - -
35A THR* 2.8 35.0 + - - +
37A HIS* 4.3 7.4 + - + +
316A LYS 4.2 0.4 - - - -
317A ARG* 2.9 46.6 + - - +
----------------------------------------------------------
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