Contacts of the strand formed by residues 13 - 24 (chain J) in PDB entry 4CDC
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 13 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J LEU 3.6 0.8 + - - -
12J LEU* 1.3 73.3 - - - +
14J THR* 1.3 63.4 + - - -
15J TRP* 3.9 5.5 + - - -
42J VAL 3.8 0.9 - - - +
43J TYR* 3.5 3.1 - - - -
44J LEU* 2.8 41.4 + - - +
117J LYS* 4.5 0.7 - - - -
119J GLY 3.6 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 14 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13J GLY* 1.3 72.8 - - - -
15J TRP* 1.3 62.1 + - - +
41J VAL* 3.8 19.1 - - + -
42J VAL 3.5 3.4 - - - +
43J TYR* 3.3 37.4 - - + -
117J LYS* 3.3 8.3 - - - +
118J VAL* 2.9 51.7 + - + -
119J GLY 3.1 10.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 15 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10J ASP 4.1 4.5 - - - -
11J LEU* 2.8 46.0 + - + +
13J GLY 4.0 6.1 - - - -
14J THR* 1.3 79.0 - - - +
16J VAL* 1.3 61.1 + - - +
17J PHE* 3.7 30.9 + + + -
40J VAL 4.1 0.2 - - - +
41J VAL* 3.5 4.5 - - - +
42J VAL* 2.8 38.2 + - + +
44J LEU* 3.8 17.5 - - + -
68J PHE* 4.7 2.2 - + - -
81J PHE* 4.2 12.1 - + - -
94J CYS 3.5 24.9 - - - -
95J ASN* 3.7 24.2 - - - -
96J GLU* 3.9 3.8 - - - -
97J THR* 3.9 18.8 - - + -
115J GLY 4.0 2.9 - - - -
116J LYS 3.6 10.8 - - - -
117J LYS* 3.6 30.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 16 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J TRP* 1.3 74.1 - - - +
17J PHE* 1.3 64.3 + - - +
18J GLN* 4.1 18.3 + - + +
39J LYS* 3.6 32.3 - - - +
40J VAL 3.8 4.3 - - - +
41J VAL* 4.6 12.6 - - + +
114J THR 4.0 0.3 - - - +
115J GLY* 3.3 4.3 - - - -
116J LYS* 2.9 38.9 + - + +
118J VAL* 3.5 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 17 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J TRP* 3.7 26.7 - + + -
16J VAL* 1.3 80.4 - - - +
18J GLN* 1.3 62.6 + - - +
19J VAL* 3.8 1.1 + - + +
38J LYS 3.7 0.9 - - - +
39J LYS* 3.3 4.9 - - - +
40J VAL* 2.7 42.1 + - - +
42J VAL* 3.8 22.2 - - + -
68J PHE* 3.9 20.0 - + - -
70J ILE* 3.8 31.6 - - + -
77J TRP* 3.3 50.9 - + + -
113J PHE* 3.9 16.6 - + + -
114J THR 3.6 0.9 - - - -
115J GLY* 3.6 16.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16J VAL* 4.4 13.7 - - + +
17J PHE* 1.3 71.6 - - - +
19J VAL* 1.3 61.4 + - - +
33J MET* 3.8 4.2 - - + +
36J GLN* 3.1 55.6 + - + +
38J LYS 3.8 10.0 + - - +
39J LYS* 3.6 26.5 - - - +
113J PHE* 3.1 23.1 - - - -
114J THR* 2.9 24.6 + - - +
116J LYS* 6.2 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I LEU* 3.8 19.1 - - + -
17J PHE 4.2 2.7 - - - +
18J GLN* 1.3 74.8 - - - +
20J GLY* 1.3 61.4 + - - +
22J SER* 5.2 7.9 - - - -
33J MET* 4.5 0.2 - - - -
36J GLN* 3.6 2.9 - - - -
37J GLU* 2.9 26.9 + - - +
38J LYS* 2.9 28.7 + - + +
40J VAL* 4.2 11.2 - - + -
77J TRP* 3.8 33.2 - - + -
102J VAL* 4.2 2.0 - - + -
111J ALA* 3.7 22.0 - - + -
112J CYS 3.5 10.5 - - - +
113J PHE* 4.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J VAL* 1.3 73.7 - - - +
21J SER* 1.3 77.2 + - - +
22J SER* 3.1 3.7 + - - -
33J MET* 3.7 12.7 - - - -
35J PRO 3.4 20.4 - - - -
37J GLU* 4.0 3.1 - - - -
111J ALA* 3.4 5.2 - - - +
112J CYS 2.9 24.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 21 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20J GLY* 1.3 74.3 - - - +
22J SER* 1.3 63.3 + - - +
24J SER* 2.7 32.7 + - - -
28J VAL* 4.8 4.7 - - - -
33J MET* 4.6 0.7 - - - +
34J GLY* 3.9 21.1 + - - -
35J PRO* 4.2 1.0 + - - +
37J GLU* 3.3 15.4 + - - -
110J TRP 3.7 5.4 - - - +
111J ALA* 3.7 1.9 - - - -
112J CYS* 4.4 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 22 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439I LEU* 6.5 0.9 - - - -
19J VAL* 5.2 7.0 - - - -
20J GLY 3.1 4.2 + - - -
21J SER* 1.3 80.8 - - - +
23J GLY* 1.3 60.7 + - - +
24J SER* 3.0 7.8 + - - -
37J GLU* 3.1 20.8 + - - +
38J LYS* 6.5 1.1 - - - -
111J ALA* 4.0 10.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 23 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314H PHE* 4.0 33.2 - - - -
22J SER* 1.3 74.8 - - - +
24J SER* 1.3 64.8 + - - +
25J GLN* 3.6 12.1 + - - +
109J ASN* 4.5 7.7 - - - +
110J TRP 3.7 5.9 + - - -
111J ALA* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 24 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21J SER* 2.7 29.4 + - - -
22J SER 3.0 1.6 + - - -
23J GLY* 1.3 80.8 - - - +
25J GLN* 1.3 70.5 + - - +
27J ASP* 6.0 0.4 - - - -
28J VAL* 4.0 18.5 - - - +
109J ASN* 3.6 6.1 - - - -
110J TRP 2.8 35.3 + - - -
----------------------------------------------------------
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