Contacts of the strand formed by residues 40 - 54 (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 TYR 40 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ASN* 4.7 0.7 - - - +
36I SER* 5.1 1.7 + - - -
38I ASP* 3.0 26.8 + - - +
39I LYS* 1.3 126.3 + - + +
41I SER* 1.3 67.4 + - - +
42I SER* 3.8 3.1 + - - -
68I ARG* 4.2 20.5 - - + +
69I THR 3.2 27.6 - - - +
70I THR* 3.7 22.1 - - + +
71I CYS 3.4 3.6 - - - +
72I PRO* 3.7 29.8 - - + -
73I LYS* 3.6 12.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 41 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33I ASN* 3.7 13.3 + - - -
40I TYR* 1.3 78.0 - - - +
42I SER* 1.3 56.2 + - - +
68I ARG* 3.8 2.8 - - - +
69I THR* 2.9 44.7 + - - -
71I CYS* 2.9 18.2 + - - -
73I LYS* 3.6 10.4 - - - +
78I LEU* 3.6 18.5 - - - +
82I GLU* 4.0 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 42 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I MET* 5.0 2.4 - - - +
32I TYR* 3.8 22.0 + - - -
33I ASN* 3.1 28.2 + - - -
36I SER* 5.3 2.6 + - - -
38I ASP* 5.2 0.7 + - - -
40I TYR 4.4 2.4 + - - -
41I SER* 1.3 74.2 + - - +
43I ARG* 1.3 62.3 - - - +
66I ILE* 3.6 22.7 - - - +
67I GLY 3.4 9.5 + - - -
68I ARG* 4.3 12.0 - - - +
69I THR* 4.7 0.4 - - - +
82I GLU* 3.9 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 43 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29I MET* 4.3 8.7 - - - -
42I SER* 1.3 71.9 - - - +
44I VAL* 1.3 76.7 + - - +
45I VAL* 4.1 15.9 - - + +
66I ILE* 3.1 5.1 - - - -
67I GLY 2.7 39.0 + - - +
69I THR* 4.0 14.9 - - + +
82I GLU* 3.5 52.7 + - - +
83I PHE* 5.9 0.7 - - - +
85I ASP* 5.6 0.4 + - - -
86I GLU* 3.6 33.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 44 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25I LEU* 4.1 18.4 - - + -
29I MET* 3.6 28.6 - - + +
43I ARG* 1.3 90.1 + - - +
45I VAL* 1.3 63.7 + - - +
46I ARG 3.5 28.3 - - - +
47I VAL* 4.0 9.2 - - + -
64I VAL* 3.6 22.7 - - + -
65I GLU 3.5 4.5 - - - -
66I ILE* 4.4 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 45 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43I ARG* 4.1 19.5 - - + +
44I VAL* 1.3 78.9 - - - +
46I ARG* 1.3 67.7 + - + +
65I GLU* 2.7 34.7 + - + +
67I GLY* 3.8 20.4 - - - +
92I TYR* 3.6 40.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 46 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44I VAL* 3.3 11.6 - - - +
45I VAL* 1.3 87.9 + - + +
47I VAL* 1.3 76.3 + - - +
48I ILE* 3.7 10.4 + - - +
64I VAL* 3.6 0.2 - - - -
65I GLU* 3.1 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 47 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I GLU* 3.3 36.3 - - + +
21I LEU* 5.2 0.7 - - + -
25I LEU* 3.7 26.9 - - + -
44I VAL* 4.0 5.4 - - + -
46I ARG* 1.3 86.2 + - - +
48I ILE* 1.3 60.0 + - - +
49I SER* 3.8 18.2 - - - +
50I ALA* 4.0 16.2 - - + -
62I LEU* 5.3 2.2 - - + -
63I GLN 3.6 7.4 - - - +
64I VAL* 3.9 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 48 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46I ARG* 4.6 9.9 - - + +
47I VAL* 1.3 73.0 - - - +
49I SER* 1.3 61.0 + - - +
63I GLN* 2.8 43.4 + - + +
64I VAL 4.2 2.5 - - - +
65I GLU* 4.4 18.8 - - + +
94I THR* 3.5 35.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 49 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47I VAL* 3.8 6.7 - - - +
48I ILE* 1.3 77.9 - - - +
50I ALA* 1.3 59.6 + - - +
51I LYS* 4.4 15.3 - - - +
61I ILE 4.4 4.2 + - - -
62I LEU* 3.6 0.7 - - - -
63I GLN* 2.8 56.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 50 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I PRO* 3.8 5.9 - - - +
14I VAL* 3.7 22.7 + - - +
16I GLU* 5.5 2.7 - - + -
21I LEU* 3.5 40.6 - - + -
47I VAL* 4.0 11.7 - - + -
49I SER* 1.3 72.5 - - - +
51I LYS* 1.4 63.4 + - - +
61I ILE 3.7 4.9 - - - -
62I LEU* 4.4 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 51 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I PRO* 4.2 26.9 + - + +
12I VAL 3.3 14.4 - - - +
13I PRO* 4.4 10.8 - - + -
14I VAL* 3.4 7.4 - - - -
21I LEU* 5.0 1.0 - - - +
49I SER* 5.2 14.4 - - - +
50I ALA* 1.4 73.9 - - - +
52I ARG* 1.3 62.1 + - - +
60I TYR* 3.3 6.1 - - - +
61I ILE* 3.0 51.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 52 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I PRO* 3.4 3.3 - - - +
12I VAL* 2.7 50.8 + - + +
13I PRO 4.6 6.5 + - - -
14I VAL* 3.3 32.9 - - + +
18I ASP* 3.7 24.4 + - - -
51I LYS* 1.3 76.1 - - - +
53I GLN* 1.3 62.6 + - - +
58I ILE* 4.1 16.3 - - + +
59I LYS 3.5 8.3 - - - +
60I TYR* 4.1 21.0 + - + -
61I ILE* 5.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 53 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I GLY 4.2 2.9 - - - +
10I ALA* 3.4 28.0 + - - +
11I PRO* 3.7 29.0 - - + +
12I VAL* 5.4 1.6 - - - -
52I ARG* 1.3 77.5 - - - +
54I LEU* 1.3 63.7 + - - +
55I VAL* 3.3 26.7 - - + +
58I ILE* 3.5 4.6 - - - +
59I LYS* 2.8 73.4 + - + +
61I ILE* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 54 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53I GLN* 1.3 79.0 - - - +
55I VAL* 1.3 65.0 + - - +
56I SER* 3.7 26.9 - - - +
57I GLY 3.7 1.3 - - - +
58I ILE* 3.7 28.5 - - + +
----------------------------------------------------------
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