Contacts of the helix formed by residues 6 - 21 (chain D) in PDB entry 4UN7
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 6 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU* 1.3 78.3 - - - +
7D VAL* 1.3 64.7 + - - +
8D SER* 3.1 4.7 + - - +
9D GLY* 3.1 5.7 + - - +
10D ILE* 2.9 42.8 + - - +
58D PHE* 3.9 21.5 - - - -
104D ARG* 4.3 18.8 - - - +
182D LEU 4.6 10.4 + - - -
183D ASN* 5.6 2.7 - - - +
184D PRO* 5.7 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 7 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU* 2.6 28.0 + - + +
6D ASN* 1.3 74.1 + - - +
8D SER* 1.3 50.9 + - - +
10D ILE* 4.2 2.8 - - - +
11D SER* 2.7 38.2 + - - +
58D PHE* 4.4 15.3 - - + -
59D LEU* 4.2 21.1 - - + +
62D GLU* 4.1 33.9 - - + +
63D LEU* 5.0 6.7 - - + -
90D TYR* 4.4 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 8 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D GLU* 3.3 26.4 + - - +
6D ASN 3.9 2.2 + - - +
7D VAL* 1.3 79.4 - - - +
9D GLY* 1.3 62.0 + - - +
11D SER* 3.6 9.0 - - - -
12D ALA* 3.0 26.9 + - - +
90D TYR* 5.1 1.6 - - - -
94D MET* 3.8 3.0 - - - +
102D ASN* 4.9 4.7 + - - -
104D ARG* 6.0 1.2 - - - +
105D GLU* 3.3 31.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 9 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ASN* 3.1 10.7 + - - +
8D SER* 1.3 79.6 + - - +
10D ILE* 1.3 61.0 + - - +
12D ALA* 3.3 0.4 + - - -
13D TYR* 2.9 26.5 + - - +
104D ARG* 5.3 5.4 - - - -
105D GLU* 5.0 6.7 - - - -
108D ALA* 3.2 21.9 - - - +
182D LEU 5.5 1.1 - - - -
183D ASN* 4.3 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 10 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ASN* 2.9 29.5 + - - +
7D VAL* 4.2 4.0 - - - +
9D GLY* 1.3 74.8 - - - +
11D SER* 1.3 65.9 + - - +
13D TYR* 3.2 3.5 + - - +
14D LEU* 2.9 38.8 + - + +
55D LEU* 3.9 42.8 - - + +
58D PHE* 3.5 35.0 - - + -
59D LEU* 5.0 4.3 - - + -
183D ASN* 5.6 0.2 - - - -
184D PRO* 3.6 27.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 11 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D VAL 2.7 21.8 + - - -
8D SER* 3.6 8.1 - - - -
10D ILE* 1.3 76.5 - - - +
12D ALA* 1.3 62.2 + - - -
14D LEU* 3.3 1.0 + - - -
15D LEU* 3.0 18.7 + - - +
59D LEU* 3.5 14.5 - - - +
90D TYR* 2.4 35.2 + - - -
91D PHE* 3.5 16.6 - - - -
94D MET* 3.7 17.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D SER 3.0 18.3 + - - +
9D GLY 3.9 2.5 - - - +
10D ILE 3.2 0.2 - - - -
11D SER* 1.3 73.2 - - - +
13D TYR* 1.3 65.6 + - - +
15D LEU* 3.1 15.4 + - - +
16D GLY 3.2 10.2 + - - -
94D MET* 3.7 15.9 - - + -
101D PHE* 4.0 7.0 - - + -
105D GLU* 3.4 35.9 - - + +
108D ALA* 4.0 0.9 - - + -
109D PHE* 3.5 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 13 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLY 2.9 14.7 + - - +
10D ILE* 3.4 10.1 - - - +
12D ALA* 1.3 76.6 - - - +
14D LEU* 1.3 65.1 + - + +
16D GLY 3.3 1.0 + - - -
17D LEU* 3.2 41.3 + - + +
51D HIS* 2.7 37.4 + + - -
55D LEU* 3.7 24.2 - - + -
108D ALA* 3.4 17.5 - - + +
111D LYS* 4.0 13.7 - - + -
112D GLY* 3.4 37.9 - - - -
115D VAL* 3.7 18.9 - - + +
184D PRO* 3.8 26.9 - - + -
186D PRO* 3.9 6.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ILE* 2.9 28.6 + - + +
11D SER 3.6 4.0 - - - +
13D TYR* 1.3 76.3 - - + +
15D LEU* 1.3 60.8 + - - +
17D LEU* 3.2 15.5 + - + +
18D ILE* 2.8 34.9 + - - +
40D ILE* 4.2 10.5 - - + +
52D ILE* 4.5 7.9 - - + +
55D LEU* 4.0 34.8 - - + +
56D MET* 3.6 32.3 - - + -
59D LEU* 3.7 24.9 - - + -
91D PHE* 4.0 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 15 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D SER 3.0 13.5 + - - +
12D ALA* 3.1 10.7 + - - +
14D LEU* 1.3 74.2 - - - +
16D GLY* 1.3 56.7 + - - +
18D ILE* 3.1 9.0 + - + +
19D ILE* 2.7 53.6 + - + +
24D LEU* 4.9 3.6 - - + -
91D PHE* 3.6 35.2 - - + +
94D MET* 4.1 25.8 - - + -
95D LEU* 4.1 24.7 - - + +
98D ILE* 5.1 0.7 - - + -
101D PHE* 4.1 13.2 - - + -
109D PHE* 3.9 16.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 16 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D ALA 3.2 8.1 + - - -
13D TYR 3.3 3.3 + - - -
15D LEU* 1.3 75.1 - - - +
17D LEU* 1.3 58.4 + - - +
19D ILE* 4.8 0.2 - - - -
20D GLY* 2.8 29.1 + - - -
109D PHE* 3.5 22.2 - - - -
113D LEU* 3.6 32.3 - - - +
116D ALA* 3.9 0.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.2 34.8 + - + +
14D LEU* 3.2 12.5 + - + +
16D GLY* 1.3 76.0 - - - +
18D ILE* 1.3 55.3 + - - +
21D ASP* 2.7 36.0 + - + +
22D GLY 3.6 0.7 + - - -
40D ILE* 3.7 21.7 - - + +
42D GLN* 6.0 3.1 - - - +
47D LEU* 6.3 0.2 - - + -
51D HIS* 5.4 0.2 - - + -
52D ILE* 3.6 37.7 - - + -
112D GLY* 3.3 28.3 - - - +
115D VAL* 3.9 21.3 - - + -
116D ALA* 4.2 8.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 18 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D LEU 2.8 21.6 + - - +
15D LEU* 3.1 6.5 + - + +
17D LEU* 1.3 77.2 - - - +
19D ILE* 1.3 64.3 + - + +
22D GLY 2.9 34.5 + - - -
23D GLY* 3.6 29.8 - - - +
24D LEU* 3.9 14.6 - - + -
38D VAL* 3.4 26.0 - - + -
39D VAL 3.9 8.5 - - - +
40D ILE* 3.7 19.3 - - + -
56D MET* 4.5 3.8 - - + -
91D PHE* 3.9 32.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15D LEU* 2.7 37.7 + - + +
16D GLY 4.3 1.1 - - - +
18D ILE* 1.3 83.1 - - + +
20D GLY* 1.3 65.2 + - - +
22D GLY 4.4 5.1 - - - +
23D GLY* 5.7 2.0 - - - -
24D LEU* 4.9 5.8 - - + -
95D LEU* 3.9 32.8 - - + -
109D PHE* 4.5 8.1 - - + -
113D LEU* 4.8 5.8 - - + -
117D GLU* 4.3 2.8 - - - +
129D ASN* 4.8 5.4 + - - +
134D LEU* 4.1 27.8 - - + -
15E G 5.1 2.1 - - - +
15F C 5.2 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 20 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16D GLY 2.8 22.8 + - - -
19D ILE* 1.3 77.1 - - - +
21D ASP* 1.3 61.6 + - - +
113D LEU* 4.0 3.5 - - - +
116D ALA* 3.5 12.1 - - - -
117D GLU* 3.3 28.8 - - - +
15E G 3.2 21.0 + - - +
15F C 4.2 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 21 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D LEU* 2.7 18.7 + - + +
20D GLY* 1.3 77.7 - - - +
22D GLY* 1.3 54.9 - - - +
40D ILE* 4.6 2.7 - - + -
41D THR* 2.7 41.3 + - - +
42D GLN* 2.2 38.5 + - - +
116D ALA* 3.4 14.8 - - + +
1197D ZN 2.6 29.1 - - - -
14E A 3.1 21.7 - - - +
15E G 3.5 9.0 - - - -
16F C 3.1 4.5 + - - -
----------------------------------------------------------
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