Contacts of the strand formed by residues 58 - 72 (chain I) in PDB entry 1CEW
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 ILE 58 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ARG* 4.1 20.9 - - + +
53I GLN 3.5 9.4 - - - +
54I LEU* 3.7 19.1 - - + -
57I GLY* 1.3 72.8 - - - -
59I LYS* 1.3 61.4 + - - +
60I TYR* 3.7 36.2 - - + +
99I VAL 3.9 0.5 - - - +
100I TYR* 3.5 2.4 - - - -
101I SER* 2.8 45.5 + - - +
103I PRO* 4.2 24.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52I ARG* 3.5 2.2 - - - -
53I GLN* 2.8 64.9 + - + +
55I VAL* 4.6 14.0 - - + +
58I ILE* 1.3 74.6 - - - +
60I TYR* 1.3 61.6 + - - +
61I ILE* 4.6 13.6 - - + +
98I VAL* 4.2 24.2 - - + -
99I VAL 3.3 9.6 - - - +
100I TYR* 4.1 16.8 - - + -
111I LEU* 5.1 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I VAL* 4.6 1.8 - - + -
18I ASP* 4.6 3.1 + - - -
20I GLY* 3.5 27.3 - - - -
21I LEU* 3.8 37.5 - - + -
23I ARG* 6.0 1.8 - - - -
24I ALA* 4.0 16.2 - - + -
51I LYS 3.3 7.9 - - - +
52I ARG* 4.1 28.8 + - + -
58I ILE* 3.7 37.6 - - + +
59I LYS* 1.3 76.1 - - - +
61I ILE* 1.3 62.3 + - - +
62I LEU* 4.0 13.7 - - + -
97I PHE 3.7 0.3 - - - +
98I VAL* 3.1 6.2 - - - +
99I VAL* 2.8 43.8 + - + +
101I SER* 4.4 11.9 - - - -
108I ILE* 6.3 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 61 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I PRO* 4.0 31.0 - - + -
49I SER* 4.0 4.4 + - - +
50I ALA* 3.7 2.8 + - - -
51I LYS* 3.0 44.4 + - + +
53I GLN* 5.1 0.9 - - + -
59I LYS* 4.6 20.9 - - - +
60I TYR* 1.3 76.7 - - - +
62I LEU* 1.3 66.5 + - - +
63I GLN* 5.6 3.4 - - + -
96I THR* 4.2 15.0 - - + -
97I PHE 3.4 8.1 - - - +
98I VAL* 4.1 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 62 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21I LEU* 3.3 33.9 - - + -
24I ALA* 4.2 16.4 - - + +
25I LEU* 3.7 28.3 - - + -
28I ALA* 4.6 1.3 - - + -
47I VAL* 5.3 2.5 - - + -
49I SER 3.6 5.2 - - - -
50I ALA* 4.4 5.4 - - + -
51I LYS 5.1 0.4 - - - +
60I TYR* 4.2 11.2 - - + -
61I ILE* 1.3 80.0 - - - +
63I GLN* 1.3 64.5 + - - +
64I VAL* 4.6 2.7 - - + -
96I THR* 3.3 6.4 - - - +
97I PHE* 2.8 46.5 + - + +
99I VAL* 3.5 31.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 3.6 0.9 - - - -
48I ILE* 2.8 58.3 + - + +
49I SER* 2.8 33.0 + - - +
61I ILE* 5.5 3.6 - - + +
62I LEU* 1.3 77.0 - - - +
64I VAL* 1.3 65.5 + - - +
94I THR* 4.6 6.7 - - - +
95I CYS 3.2 5.8 + - - +
96I THR* 4.0 17.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 64 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 3.6 28.7 - - + -
29I MET* 4.8 1.3 - - - -
44I VAL* 3.6 32.3 - - + -
46I ARG 3.6 2.0 - - - -
47I VAL* 3.9 13.0 - - + -
48I ILE* 4.2 4.0 - - - +
62I LEU* 4.6 1.8 - - + -
63I GLN* 1.3 88.0 - - - +
65I GLU* 1.3 59.1 + - - +
66I ILE* 3.3 29.9 + - + +
94I THR* 3.3 2.8 - - - +
95I CYS 2.7 41.0 + - - +
97I PHE* 4.4 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 65 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I VAL* 3.5 4.2 - - - -
45I VAL* 2.7 49.5 + - + +
46I ARG* 3.1 37.9 + - + +
48I ILE* 4.4 12.3 - - + +
64I VAL* 1.3 70.8 - - - +
66I ILE* 1.3 57.6 + - - +
92I TYR* 3.8 31.0 - - + +
93I THR 3.3 6.3 - - - -
94I THR* 4.1 15.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 66 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I MET* 3.5 30.5 - - + -
32I TYR* 4.1 16.8 - - + +
42I SER* 3.6 25.4 - - - +
43I ARG 3.1 10.8 - - - +
45I VAL* 4.4 2.0 - - - -
64I VAL* 3.3 22.9 - - + +
65I GLU* 1.3 74.8 - - - +
67I GLY* 1.3 63.8 + - - +
92I TYR* 3.3 4.5 - - - -
93I THR* 2.7 38.4 + - - +
95I CYS* 3.3 39.3 - - + -
97I PHE* 4.1 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 67 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42I SER* 3.4 4.6 - - - -
43I ARG* 2.7 38.1 + - - +
45I VAL* 3.8 10.1 - - - +
66I ILE* 1.3 78.2 - - - +
68I ARG* 1.3 63.8 + - - -
69I THR* 3.7 0.7 + - - +
91I LYS 3.4 7.6 - - - -
92I TYR* 4.1 13.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 68 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I ASP* 2.7 59.3 + - - +
39I LYS* 5.6 2.2 - - - +
40I TYR* 4.2 20.1 - - + +
41I SER 3.8 10.1 - - - +
42I SER* 4.3 9.2 - - - +
67I GLY* 1.3 72.4 - - - -
69I THR* 1.3 70.0 + - - +
89I MET* 3.3 25.8 - - - +
90I ALA* 3.4 28.0 + - + +
91I LYS* 3.1 16.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 69 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I TYR* 3.2 22.5 - - - +
41I SER* 2.9 27.6 + - - +
43I ARG* 4.0 35.7 - - + +
67I GLY 4.6 0.4 - - - +
68I ARG* 1.3 79.0 + - - +
70I THR* 1.3 64.0 + - - +
71I CYS* 3.0 27.0 + - - +
82I GLU* 4.1 13.2 - - + -
85I ASP* 3.7 20.6 - - - +
89I MET* 4.4 1.3 - - - -
90I ALA* 5.6 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I TYR* 3.7 23.1 - - + +
69I THR* 1.3 75.5 - - - +
71I CYS* 1.3 59.8 + - - +
72I PRO* 3.4 10.2 - - - +
81I CYS* 4.4 4.9 - - - -
85I ASP* 3.2 14.1 + - - +
89I MET* 3.0 40.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 71 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40I TYR* 3.9 2.0 - - - -
41I SER* 2.9 26.9 + - - -
69I THR* 3.0 16.0 + - - +
70I THR* 1.3 75.6 - - - +
72I PRO* 1.3 69.4 - - + +
75I SER* 5.8 0.2 - - - +
78I LEU* 4.3 14.4 - - + -
81I CYS* 2.0 60.3 - - + -
82I GLU* 3.7 8.3 - - + -
85I ASP* 3.7 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 72 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I LYS* 3.2 16.4 - - + +
40I TYR* 3.7 15.5 - - + -
70I THR 3.4 10.8 - - - +
71I CYS* 1.3 85.6 - - + +
73I LYS* 1.3 53.8 + - - +
74I SER* 2.7 25.7 + - - +
75I SER* 2.8 32.9 + - - +
77I ASP* 5.9 1.1 - - - +
78I LEU* 4.1 9.0 - - - +
81I CYS* 5.3 1.3 - - - -
----------------------------------------------------------
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