Contacts of the helix formed by residues 72 - 87 (chain A) in PDB entry 1KYZ
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 ASP 72 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 2.9 19.2 + - - +
71A PRO* 1.3 84.1 - - - +
73A ALA* 1.3 66.5 + - - +
74A PRO* 3.3 2.8 - - - -
75A VAL* 3.4 10.1 + - + +
76A MET* 3.1 32.2 + - + +
150E GLY* 5.4 3.3 - - - -
151E GLY 5.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 73 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A ALA* 4.1 13.2 - - + -
66A LEU* 4.8 0.4 - - + -
68A THR* 4.6 9.6 - - + -
70A ASN* 3.1 25.2 + - + +
72A ASP* 1.3 76.8 - - - +
74A PRO* 1.3 69.1 - - + +
76A MET* 3.3 4.3 + - - +
77A LEU* 2.9 30.0 + - + +
147E VAL* 4.1 28.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 74 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.3 21.7 - - + +
60A ILE* 3.9 36.6 - - + +
63A ALA* 3.7 16.1 - - + -
70A ASN 4.1 1.6 - - - +
71A PRO* 3.4 15.3 - - + +
72A ASP 3.4 4.3 - - - -
73A ALA* 1.3 93.8 - - + +
75A VAL* 1.3 60.2 + - + +
77A LEU* 3.1 2.5 + - + +
78A ASP* 2.8 25.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASP* 3.4 11.3 + - + +
74A PRO* 1.3 77.3 - - + +
76A MET* 1.3 64.3 + - + +
78A ASP* 3.2 8.9 + - + +
79A ARG* 3.2 38.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 76 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ASN* 4.2 9.0 - - - -
72A ASP* 3.1 24.7 - - + +
73A ALA* 3.3 6.0 + - - +
75A VAL* 1.3 77.8 - - + +
77A LEU* 1.3 62.9 + - - +
79A ARG* 3.3 3.6 + - - +
80A MET* 3.2 26.6 + - - +
143E LEU* 4.6 4.5 - - + -
146E ALA* 3.8 43.7 - - + +
147E VAL* 4.1 21.8 - - + +
150E GLY* 5.6 0.7 - - - -
151E GLY 4.1 9.4 - - - +
153E PRO* 5.1 2.9 - - + -
321E LEU* 3.6 36.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 77 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A LEU* 4.2 8.7 - - + -
44A LEU* 3.8 33.0 - - + -
59A PRO* 4.0 5.6 - - + +
62A ILE* 4.2 8.5 - - + -
63A ALA* 3.7 27.6 - - + +
66A LEU* 3.6 22.2 - - + -
73A ALA 2.9 21.7 + - - +
74A PRO* 3.5 3.1 - - + +
76A MET* 1.3 74.4 - - - +
78A ASP* 1.3 58.3 + - - +
80A MET* 3.1 9.4 + - - -
81A LEU* 2.8 50.0 + - + +
147E VAL* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 78 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A PRO* 3.6 21.6 - - + +
74A PRO 2.8 13.5 + - - +
75A VAL* 3.2 14.8 + - + +
77A LEU* 1.3 75.2 - - - +
79A ARG* 1.3 58.8 + - + +
81A LEU* 4.3 1.6 - - - -
82A ARG* 2.9 30.9 + - - +
103A GLN* 6.0 0.2 - - - -
104A ARG* 2.6 40.4 + - - +
106A TYR* 2.8 35.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A VAL* 3.2 29.6 + - + +
76A MET* 3.6 6.1 - - - +
77A LEU 3.2 0.2 - - - -
78A ASP* 1.3 78.8 - - + +
80A MET* 1.3 61.1 + - - +
82A ARG* 3.7 19.0 + - - +
83A LEU 3.5 10.2 + - - -
314E VAL* 4.8 0.7 - - - +
317E ASP* 2.8 60.6 + - - +
318E VAL* 3.5 18.6 - - + +
320E MET* 3.7 0.4 - - - +
321E LEU* 3.5 41.2 - - + +
324E ASN 5.7 1.0 + - - -
326E GLY 5.8 0.8 - - - -
327E GLY 3.0 27.4 + - - -
328E LYS* 3.5 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A ILE* 3.8 26.7 - - + +
38A SER* 3.8 19.5 - - - -
39A ALA* 4.1 14.4 - - + +
42A LEU* 4.2 10.8 - - + -
44A LEU* 4.7 5.8 - - + -
76A MET 3.2 15.6 + - - +
77A LEU* 3.1 22.3 + - - +
79A ARG* 1.3 74.1 - - - +
81A LEU* 1.3 67.7 + - + +
83A LEU* 3.1 15.1 + - - +
84A LEU* 3.3 15.5 + - + +
143E LEU* 3.8 29.8 - - + -
147E VAL* 4.2 11.9 - - - -
318E VAL* 4.6 4.3 - - - -
321E LEU* 3.9 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A LEU* 4.0 26.5 - - + -
45A LEU* 6.3 0.7 - - + -
48A ILE* 4.5 5.6 - - + -
59A PRO* 4.3 5.8 - - + -
62A ILE* 3.9 26.5 - - + -
77A LEU* 2.8 40.7 + - + +
78A ASP 4.2 0.7 - - - +
80A MET* 1.3 68.9 - - - +
82A ARG* 1.3 59.9 + - - +
84A LEU* 3.0 9.7 + - + +
85A ALA* 2.8 29.3 + - - +
90A LEU* 3.4 25.6 - - + +
106A TYR* 3.5 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP* 2.9 18.5 + - - +
79A ARG* 3.8 21.9 + - - +
81A LEU* 1.3 75.3 - - - +
83A LEU* 1.3 63.8 + - - +
85A ALA* 3.2 3.5 + - - +
86A CYS* 3.0 23.0 + - - -
104A ARG* 3.8 38.0 - - - +
106A TYR* 3.3 15.8 + - - +
300E LEU* 3.4 35.3 - - - +
301E PRO 5.1 5.8 + - - -
302E VAL 5.4 1.1 - - - -
303E ALA 6.0 0.4 - - - -
304E PRO* 4.1 16.6 - - + +
314E VAL* 4.2 22.2 - - + +
317E ASP* 3.1 32.9 + - - -
329E GLU 5.4 0.4 + - - -
331E THR* 6.1 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31A VAL* 3.6 30.5 - - + +
32A LEU* 4.0 12.1 - - - -
35A ILE* 3.7 24.2 - - + -
79A ARG 3.5 1.8 + - - -
80A MET 3.1 10.3 + - - +
82A ARG* 1.3 81.7 - - - +
84A LEU* 1.3 64.9 + - + +
86A CYS* 3.2 4.9 + - + +
87A TYR* 3.2 34.5 + - + -
311E LYS* 5.9 0.2 - - - -
314E VAL* 3.6 25.1 - - + +
315E HIS* 3.7 30.7 - - + +
318E VAL* 4.1 11.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 4.4 7.6 - - + -
35A ILE* 4.0 18.4 - - + -
36A LEU* 4.0 21.5 - - + +
39A ALA* 3.9 26.7 - - + -
44A LEU* 5.7 0.2 - - + -
45A LEU* 5.3 3.4 - - + -
80A MET* 3.7 13.9 - - + +
81A LEU* 3.0 12.9 + - + +
83A LEU* 1.3 75.7 - - + +
85A ALA* 1.3 63.6 + - - +
87A TYR* 3.2 2.8 + - - +
88A ILE 3.1 4.3 + - - -
89A ILE* 2.9 56.1 + - + +
90A LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81A LEU 2.8 15.7 + - - +
82A ARG 3.5 5.2 - - - +
84A LEU* 1.3 73.9 - - - +
86A CYS* 1.3 65.8 + - - +
88A ILE* 3.0 23.0 + - - +
90A LEU* 3.3 20.4 - - - +
92A CYS* 4.0 11.0 - - + -
106A TYR* 3.9 20.6 - - + -
304E PRO* 3.9 16.3 - - + -
305E ASP 5.5 0.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG 3.0 17.7 + - - -
83A LEU* 3.2 10.3 + - + +
85A ALA* 1.3 77.8 - - - +
87A TYR* 1.3 58.0 + - + +
88A ILE* 3.4 3.1 + - - +
304E PRO* 3.9 15.7 - - - -
305E ASP 3.4 24.0 - - - +
306E SER* 3.4 18.2 + - - -
310E THR* 4.0 8.1 - - - -
311E LYS* 3.4 30.4 - - + -
314E VAL* 3.7 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A GLN* 2.9 32.5 + - - +
32A LEU* 3.9 45.7 - - + +
83A LEU* 3.2 34.2 + - + +
84A LEU 3.2 7.4 + - - +
85A ALA 3.1 0.6 - - - -
86A CYS* 1.3 80.4 - - + +
88A ILE* 1.3 70.7 + - - +
89A ILE* 3.4 7.6 + - + +
9E ILE* 4.0 6.1 - - + +
10E THR* 3.4 25.2 + - - -
11E PRO 4.7 4.3 - - - +
22E PHE* 4.0 18.0 - + + -
26E LEU* 6.0 0.2 - - + -
311E LYS* 3.7 22.6 - - + +
315E HIS* 2.6 36.9 + - - -
----------------------------------------------------------
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