Contacts of the strand formed by residues 6 - 19 (chain E) in PDB entry 5HJD
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 ALA 6 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4E SER* 6.1 0.9 - - - -
5E CYS* 1.3 75.6 - - - +
7E VAL* 1.3 63.4 + - - +
8E GLN* 3.7 7.3 + - + +
123E THR* 4.4 16.2 - - + -
124E PHE 3.5 5.2 - - - -
125E ASN* 4.4 8.1 - - - +
4G SER 3.2 11.1 - - - +
6G ALA* 3.4 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5E CYS* 3.8 23.3 - - - -
6E ALA* 1.3 71.2 - - - +
8E GLN* 1.3 70.7 + - - +
9E VAL* 4.6 2.2 - - + -
122E LEU 3.6 0.9 - - - +
123E THR* 3.6 1.3 - - - -
124E PHE* 2.8 41.2 + - + +
127E PRO* 3.9 16.8 - - + -
132E ARG* 4.1 16.2 - - + -
135E LEU* 3.8 37.2 - - + -
136E LEU* 4.7 9.0 - - + -
3G SER* 5.2 0.2 - - - -
4G SER 3.3 9.9 - - - +
5G CYS* 4.2 7.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 8 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6E ALA* 4.4 8.3 - - + +
7E VAL* 1.3 77.2 - - - +
9E VAL* 1.3 63.3 + - - +
10E LYS* 5.7 0.8 - - + +
121E LYS* 3.2 42.9 + - + +
122E LEU 3.2 5.2 - - - +
123E THR* 3.7 23.3 + - + +
2G ALA 3.8 0.9 - - - +
3G SER* 3.2 26.0 - - - -
4G SER* 3.2 24.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 9 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E VAL* 4.2 2.7 + - + -
8E GLN* 1.3 77.2 - - - +
10E LYS* 1.3 65.3 + - - +
11E LEU* 5.3 0.2 - - + -
47E PHE* 4.1 22.9 - - + -
121E LYS* 3.7 4.3 - - - +
122E LEU* 2.9 60.6 + - + +
124E PHE* 4.0 11.2 - - + -
135E LEU* 3.7 30.7 - - + +
138E ALA* 5.4 0.7 - - + -
2G ALA 3.7 4.3 - - - +
3G SER* 3.6 21.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 10 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121C LYS* 5.8 8.3 - - - +
8E GLN 5.7 0.9 - - - +
9E VAL* 1.3 78.9 - - - +
11E LEU* 1.3 72.2 + - - +
12E GLU* 6.2 0.4 - - + -
38E GLY* 4.3 0.7 - - - -
39E PRO* 3.4 37.6 - - + +
44E ILE* 4.8 2.6 - - - +
120E GLU 3.6 6.1 - - - +
121E LYS* 5.3 11.2 - - + -
2G ALA* 3.6 33.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 11 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9E VAL* 4.2 0.9 + - + -
10E LYS* 1.3 83.6 - - - +
12E GLU* 1.3 67.5 + - - +
13E LEU* 4.4 9.6 - - + -
36E VAL* 4.7 7.0 - - + -
37E ARG 3.7 5.8 - - - +
38E GLY* 5.4 0.2 - - - -
44E ILE* 3.9 35.4 - - + -
47E PHE* 4.3 11.7 - - + -
48E VAL* 5.1 0.4 - - + -
87E VAL* 4.2 30.7 - - + -
100E PHE* 4.4 10.3 - - + -
119E CYS* 3.6 1.6 - - - +
120E GLU* 2.8 40.5 + - + +
122E LEU* 3.6 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 12 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118C ARG* 5.1 1.2 - - - -
119C CYS* 4.2 10.0 + - - +
10E LYS* 6.2 0.4 - - + -
11E LEU* 1.3 80.0 - - - +
13E LEU* 1.3 62.3 + - - +
35E PHE* 3.8 1.7 - - - +
36E VAL* 3.3 4.5 - - - +
37E ARG* 2.8 76.4 + - + +
38E GLY 3.6 5.5 - - - +
39E PRO* 4.0 24.9 - - + +
117E LEU* 4.1 20.5 - - + +
118E ARG 3.6 2.7 - - - -
119E CYS* 3.7 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 13 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E LEU* 4.4 13.0 - - + -
12E GLU* 1.3 85.9 - - - +
14E GLY* 1.3 56.2 + - - +
35E PHE 3.3 5.4 - - - +
36E VAL* 3.7 22.7 - - + -
85E ILE* 3.7 24.5 - - + -
100E PHE* 3.7 46.9 - - + -
102E TYR* 4.1 18.6 - - + -
117E LEU* 3.8 3.0 - - - +
118E ARG* 2.7 52.8 + - + +
120E GLU* 4.6 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13E LEU* 1.3 74.8 - - - +
15E HIS* 1.3 62.1 + - - -
34E VAL* 3.2 4.9 - - - +
35E PHE* 2.8 51.0 + - - -
102E TYR* 3.3 11.5 - - - -
116E HIS 3.1 14.6 - - - -
117E LEU* 4.4 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14E GLY* 1.3 75.2 - - - +
16E ARG* 1.3 71.5 + - - +
17E ALA* 4.2 1.6 - - + -
33E MET 3.1 14.1 - - - +
34E VAL* 3.7 15.0 - - + -
35E PHE* 3.8 4.8 - - - -
102E TYR* 2.4 36.9 + + + +
103E ASP 3.9 5.4 - - - -
104E LEU* 3.7 21.5 - - + -
105E PHE* 2.9 58.2 + + - -
114E VAL* 3.3 18.4 - - + +
115E ASN* 3.7 3.6 - - - +
116E HIS* 3.2 29.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 16 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112C PRO* 4.6 23.0 - - - +
113C PRO* 5.1 13.2 + - - +
115C ASN* 4.9 19.6 - - + +
15E HIS* 1.3 77.0 - - - +
17E ALA* 1.3 61.3 + - - +
18E GLN* 4.3 23.4 + - + +
32E TRP* 3.1 9.1 - - - +
33E MET* 2.8 58.9 + - + +
35E PHE* 5.7 3.6 - - + -
114E VAL 3.2 9.2 - - - +
115E ASN* 3.8 22.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 17 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E HIS* 4.2 5.6 - - + -
16E ARG* 1.3 77.5 - - - +
18E GLN* 1.3 61.6 + - - +
30E HIS* 4.9 5.2 - - + -
31E ASP 3.3 5.6 - - - +
32E TRP* 4.2 3.4 - - + -
106E LEU* 3.6 31.6 - - + -
107E HIS* 5.6 0.3 + - - +
113E PRO* 3.7 4.3 - - - +
114E VAL* 3.0 51.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 18 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113C PRO* 5.4 10.9 - - - +
115C ASN* 6.2 0.2 - - - +
16E ARG* 4.3 21.9 + - + +
17E ALA* 1.3 75.5 - - - +
19E VAL* 1.3 64.4 + - - +
30E HIS* 3.2 10.2 - - - +
31E ASP* 2.7 46.8 + - + +
113E PRO* 3.8 27.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 19 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18E GLN* 1.3 80.9 - - - +
20E ARG* 1.3 72.1 + - - +
29E THR* 3.5 8.7 - - - +
30E HIS* 3.3 31.2 - - + +
31E ASP* 5.7 0.4 - - - -
107E HIS 4.9 1.3 - - - +
108E LEU 5.0 1.8 - - - +
109E GLU* 4.8 29.8 - - + +
111E HIS 5.9 2.9 - - - +
113E PRO* 5.8 0.4 - - - +
----------------------------------------------------------
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