Contacts of the helix formed by residues 2 - 17 (chain K) in PDB entry 5G04
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 ASN 2 (chain K).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194J CYS* 6.2 2.2 - - - -
196J GLU* 3.6 25.1 - - + +
197J GLU* 3.9 23.0 - - + +
3K LEU* 1.3 68.0 + - - +
4K GLU* 3.3 7.7 - - - +
5K ARG* 3.4 10.5 + - - +
6K LEU* 3.0 31.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 3 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K ASN* 1.3 78.1 - - - +
4K GLU* 1.4 57.9 + - - +
6K LEU* 3.3 10.0 + - - +
7K ARG* 2.9 59.5 + - - +
29K VAL* 5.1 3.6 - - + +
32K LEU* 6.1 3.6 - - + -
33K SER* 5.2 10.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 4 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2K ASN 3.3 4.8 - - - +
3K LEU* 1.4 77.2 - - - +
5K ARG* 1.3 63.7 + - - +
7K ARG* 3.1 18.2 + - - +
8K LYS* 3.0 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 5 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197J GLU* 4.2 15.0 - - - +
2K ASN* 3.4 13.1 + - - +
4K GLU* 1.3 78.9 - - - +
6K LEU* 1.3 57.9 + - + +
8K LYS* 3.4 7.1 + - - +
9K ARG* 3.0 33.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 6 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162J TYR* 3.9 24.9 - - + +
197J GLU* 5.4 5.6 - - + +
200J LEU* 4.2 13.5 - - + -
2K ASN* 3.0 22.6 + - + +
3K LEU* 3.6 8.5 - - - +
4K GLU 3.2 0.2 - - - -
5K ARG* 1.3 73.8 - - - +
7K ARG* 1.3 60.6 + - - +
9K ARG* 3.2 8.1 + - + +
10K VAL* 2.8 29.3 + - - +
25K TRP* 3.6 34.7 - - + +
29K VAL* 3.9 20.7 - - + +
32K LEU* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 7 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3K LEU* 2.9 38.0 + - - +
4K GLU* 3.1 15.4 + - - +
6K LEU* 1.3 74.0 - - - +
8K LYS* 1.3 65.6 + - - +
10K VAL* 3.3 13.1 - - + +
11K ARG* 3.0 31.6 + - + +
29K VAL* 4.0 10.8 - - + +
33K SER* 3.3 12.9 + - - -
36K GLU* 4.1 12.6 + - - -
39K ASP* 3.3 39.2 + - - +
42K TRP* 5.5 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 8 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4K GLU 3.0 12.9 + - - +
5K ARG* 3.7 10.8 - - - +
7K ARG* 1.3 75.4 - - - +
9K ARG* 1.3 57.3 + - + +
11K ARG* 3.3 9.2 + - + +
12K GLN* 2.9 73.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 9 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J SER* 4.9 10.3 - - - -
160J ASP* 3.7 21.4 + - - -
162J TYR* 4.0 45.4 - - + +
5K ARG* 3.0 27.9 + - + +
6K LEU* 3.3 15.7 - - + +
8K LYS* 1.3 74.6 - - + +
10K VAL* 1.3 65.0 + - - +
12K GLN* 3.4 25.0 + - - +
13K TYR* 2.8 49.6 + - + -
16K GLN* 4.7 9.7 + - - -
25K TRP* 6.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 10 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6K LEU 2.8 18.6 + - - +
7K ARG* 3.3 19.5 - - + +
9K ARG* 1.3 73.7 - - - +
11K ARG* 1.3 70.5 + - + +
13K TYR* 3.3 7.9 + - - +
14K LEU* 3.2 24.7 + - + +
22K ALA* 3.1 36.1 - - + +
25K TRP* 4.4 9.5 - - + +
26K ALA* 3.7 23.1 - - + +
29K VAL* 4.7 9.2 - - + -
42K TRP* 4.9 15.5 - - + -
46K CYS* 4.8 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 11 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15J ASP* 5.1 6.3 + - - -
7K ARG* 3.0 23.9 + - - +
8K LYS* 3.9 9.9 - - + +
10K VAL* 1.3 75.1 - - + +
12K GLN* 1.3 61.5 + - - +
14K LEU* 3.3 13.0 + - + +
15K ASP* 3.0 26.5 + - - +
42K TRP* 3.4 59.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 12 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J SER 6.1 1.2 - - - +
8K LYS* 2.9 57.9 + - - +
9K ARG* 3.5 32.2 + - - +
11K ARG* 1.3 76.6 - - - +
13K TYR* 1.3 56.2 + - + +
15K ASP* 3.4 12.4 + - + +
16K GLN* 2.9 46.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160J ASP* 3.0 30.8 + - - -
162J TYR* 3.3 9.7 - - + +
163J CYS* 3.0 34.4 + - + -
9K ARG* 2.8 56.2 + - + -
10K VAL* 3.5 9.9 - - - +
11K ARG 3.2 0.4 - - - -
12K GLN* 1.3 75.3 - - - +
14K LEU* 1.3 52.6 + - - +
16K GLN* 3.2 13.2 + - - +
17K GLN 2.8 28.4 + - - -
18K GLN* 2.9 38.0 + - + +
21K SER* 3.3 25.8 - - - -
22K ALA* 3.7 16.6 - - + -
25K TRP* 5.2 7.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10K VAL* 3.2 15.8 + - + +
11K ARG* 3.4 14.6 - - + +
13K TYR* 1.3 75.5 - - - +
15K ASP* 1.3 66.6 + - - +
17K GLN* 3.0 15.2 + - - +
19K TYR* 3.9 30.5 + - + -
22K ALA* 3.8 18.8 - - + -
42K TRP* 4.5 20.2 - - + +
45K GLN* 4.5 21.5 - - + -
46K CYS* 4.1 11.2 - - - -
49K LEU* 3.9 20.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 15 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11J ARG* 5.1 6.3 + - - -
41J TYR* 5.5 2.6 + - - -
42J TRP* 4.4 19.1 - - - -
45J GLN* 5.2 7.1 + - - -
11K ARG 3.0 12.9 + - - +
12K GLN* 3.5 17.9 - - - +
14K LEU* 1.3 74.3 - - - +
16K GLN* 1.3 69.6 + - - +
17K GLN* 3.3 3.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J TYR* 4.3 10.0 - - - -
78J ARG* 4.2 2.3 + - - -
124J SER* 5.6 0.5 - - - -
127J SER* 3.1 44.6 + - - +
128J ILE* 5.2 8.1 - - + -
131J SER* 5.0 3.8 + - - +
160J ASP* 5.0 2.0 + - - -
9K ARG* 4.7 5.2 + - - -
12K GLN* 2.9 37.1 + - - +
13K TYR* 3.5 19.6 - - - +
15K ASP* 1.3 83.2 - - - +
17K GLN* 1.3 68.7 + - - +
18K GLN* 3.4 26.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain K).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41J TYR* 5.6 0.3 + - - -
45J GLN* 2.9 33.2 + - - +
48J TYR* 3.2 33.9 - - - -
49J LEU* 4.5 10.5 - - - +
74J TYR* 5.1 2.4 - - - -
75J LEU* 4.5 4.7 - - - +
78J ARG* 2.9 51.0 + - - +
13K TYR 2.8 3.4 + - - -
14K LEU 3.0 13.3 + - - +
15K ASP 3.1 2.4 - - - +
16K GLN* 1.3 81.4 - - - +
18K GLN* 1.3 60.6 + - - +
19K TYR* 3.1 41.0 + - + +
----------------------------------------------------------
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