Contacts of the helix formed by residues 14 - 30 (chain A) in PDB entry 1YPN
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 PRO 14 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A GLN 4.4 1.6 - - - +
13A SER* 1.3 89.0 - - - +
15A LEU* 1.3 57.2 + - - +
17A LEU* 3.3 9.5 + - + +
18A TRP* 3.0 25.3 + - - +
151A ASN* 4.2 13.9 - - + +
177A LEU* 4.2 17.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ARG* 6.2 0.2 - - - +
13A SER* 3.2 6.1 + - - +
14A PRO* 1.3 76.7 - - - +
16A ALA* 1.3 66.6 + - - +
18A TRP* 3.0 15.8 + - + +
19A GLN* 3.1 27.3 + - + +
81A SER* 5.7 1.1 - - - +
152A VAL* 4.1 18.8 - - + -
173A GLY* 4.0 19.7 - - - +
176A ARG* 4.2 25.4 - - + +
177A LEU* 3.9 29.5 - - + +
314A DPM 3.9 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 3.4 14.3 + - - +
11A ARG* 3.4 42.4 - - + +
13A SER* 3.2 19.3 + - - +
15A LEU* 1.3 77.2 - - - +
17A LEU* 1.3 61.9 + - - +
19A GLN* 3.2 17.6 + - - +
20A ALA 3.1 17.7 + - - -
79A VAL* 5.6 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A THR* 4.3 12.8 - - + -
11A ARG 4.0 15.3 - - - +
12A GLN* 3.4 26.2 - - + +
13A SER 3.0 15.5 + - - +
14A PRO* 3.7 7.6 - - + +
16A ALA* 1.3 73.6 - - - +
18A TRP* 1.3 65.4 + - - +
20A ALA* 3.6 4.1 - - + +
21A HIS* 3.1 35.0 + - + +
38A LEU* 4.8 15.3 - - + -
40A PRO* 4.4 13.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A PRO 3.0 12.8 + - - +
15A LEU* 3.0 16.5 + - + +
17A LEU* 1.3 76.5 - - - +
19A GLN* 1.3 68.6 + - + +
21A HIS* 3.4 6.8 + - - +
22A TYR* 2.9 62.5 + + + -
102A GLU* 3.9 10.3 - - - -
176A ARG* 3.2 74.8 + - + -
177A LEU* 4.7 5.6 - - + -
201A VAL* 5.3 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A LEU* 3.1 21.5 + - + +
16A ALA* 3.2 15.5 + - - +
18A TRP* 1.3 90.2 - - + +
20A ALA* 1.3 64.0 + - - +
22A TYR* 3.3 3.6 + - - +
23A VAL* 3.1 29.3 + - - +
79A VAL* 4.0 16.3 - - + +
80A HIS* 4.1 6.1 - - - -
81A SER* 3.0 37.6 + - - -
176A ARG* 3.7 13.7 - - - +
201A VAL* 3.5 29.6 - - + +
314A DPM 4.2 2.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.5 7.3 - - + +
10A THR* 4.0 28.3 - - + +
16A ALA 3.1 12.4 + - - +
17A LEU* 3.6 9.9 - - - +
18A TRP 3.3 0.2 - - - -
19A GLN* 1.3 78.3 - - - +
21A HIS* 1.3 57.6 + - - +
23A VAL* 3.3 5.4 + - - +
24A LYS* 2.8 29.5 + - - +
38A LEU* 4.0 22.0 - - + -
79A VAL* 4.6 9.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.1 28.2 + - + +
18A TRP* 3.8 5.8 - - - +
20A ALA* 1.3 74.9 - - - +
22A TYR* 1.3 66.1 + - - +
24A LYS* 3.5 27.3 + - + +
25A ASP* 2.9 40.8 + - - +
38A LEU* 4.1 21.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 2.9 49.5 + + + +
19A GLN 3.4 8.1 - - - +
21A HIS* 1.3 78.8 - - - +
23A VAL* 1.3 74.0 + - + +
25A ASP* 4.6 1.6 - - - -
26A LYS* 2.9 71.7 + - + +
99A CYS* 4.0 35.1 - - + +
100A GLU* 4.3 15.2 + - - +
102A GLU* 5.2 9.9 + - - -
176A ARG* 6.0 0.7 - - - -
201A VAL* 4.3 11.4 - - + -
219A LEU* 6.2 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.3 10.3 - - + -
19A GLN 3.1 16.0 + - - +
20A ALA 3.7 3.8 - - - +
22A TYR* 1.3 91.0 - - + +
24A LYS* 1.3 62.7 + - - +
26A LYS* 3.1 4.9 + - - +
27A LEU* 2.9 35.4 + - + +
77A ILE* 4.4 5.4 - - + -
79A VAL* 4.0 24.0 - - + -
99A CYS* 4.8 2.0 - - - -
201A VAL* 4.3 10.1 - - + -
203A ILE* 3.9 18.4 - - + -
219A LEU* 3.8 21.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A ILE* 4.6 3.6 - - + +
20A ALA 2.8 20.2 + - - +
21A HIS* 3.5 28.5 + - + +
23A VAL* 1.3 72.7 - - - +
25A ASP* 1.3 64.0 + - - +
27A LEU* 3.3 5.7 + - - +
28A MET* 2.9 39.7 + - + +
36A VAL* 3.8 49.9 + - + +
38A LEU* 4.4 16.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A HIS* 2.9 31.9 + - - +
22A TYR* 4.6 1.4 - - - -
23A VAL 3.2 0.2 - - - -
24A LYS* 1.3 81.7 - - - +
26A LYS* 1.3 78.4 + - - +
28A MET* 3.3 8.2 + - - +
29A ALA* 2.8 30.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 26 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A TYR* 2.9 72.7 + - + +
23A VAL* 3.1 7.5 + - - +
25A ASP* 1.3 92.2 + - - +
27A LEU* 1.3 61.5 + - - +
29A ALA* 3.6 7.7 - - + +
30A SER* 3.3 26.7 + - - -
219A LEU* 3.8 24.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 27 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A LEU* 3.4 29.4 - - + -
8A ILE* 4.6 6.1 - - + -
23A VAL* 2.9 32.9 + - + +
24A LYS* 3.6 6.3 - - - +
26A LYS* 1.3 75.8 - - - +
28A MET* 1.3 54.7 + - - +
30A SER 3.3 1.4 + - - -
31A HIS* 2.7 51.0 + - - +
34A LEU* 4.3 16.4 - - + -
36A VAL* 4.6 6.1 - - + -
77A ILE* 4.5 2.2 - - + -
215A LEU* 3.6 31.6 - - + +
216A LEU* 4.4 11.4 - - + -
219A LEU* 4.1 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 28 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A LYS* 2.9 34.1 + - + +
25A ASP* 3.8 8.1 - - - +
27A LEU* 1.3 75.6 - - - +
29A ALA* 1.3 63.8 + - - +
31A HIS 3.0 24.3 - - - +
32A PRO* 3.1 31.9 - - - +
34A LEU* 3.0 31.2 - - - +
36A VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 29 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A ASP 2.8 18.1 + - - +
26A LYS* 3.6 12.8 - - + +
28A MET* 1.3 79.6 - - - +
30A SER* 1.3 61.2 + - - +
32A PRO* 4.4 8.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 30 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26A LYS 3.3 15.4 + - - -
27A LEU* 3.3 2.7 + - - -
29A ALA* 1.3 78.1 - - - +
31A HIS* 1.3 83.6 + - - +
32A PRO* 3.7 6.1 - - - +
218A ALA* 4.0 21.5 + - - +
219A LEU* 4.9 2.7 - - - +
----------------------------------------------------------
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