Contacts of the helix formed by residues 15 - 29 (chain B) in PDB entry 1ZMD
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 15 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLY 3.4 2.8 + - - -
14B SER* 1.3 78.9 - - - +
16B PRO* 1.3 77.0 - - - +
18B GLY 3.0 1.1 + - - +
19B TYR* 2.8 25.4 + - - -
42B GLY 3.7 7.9 - - - -
480B FAD 3.2 31.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 16 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY* 1.3 82.9 - - - +
17B GLY* 1.3 62.3 + - - +
19B TYR* 4.0 11.2 - - + -
20B VAL* 3.2 27.5 - - - +
42B GLY 3.7 10.5 - - - +
45B CYS* 3.4 25.6 - - + -
328B ALA* 3.7 18.2 - - + +
331B ALA* 4.3 0.2 - - + -
332B GLU* 3.5 29.3 - - + +
480B FAD 3.3 33.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 17 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B PRO* 1.3 75.3 - - - +
18B GLY* 1.3 57.1 + - - +
20B VAL* 4.1 0.5 - - - +
21B ALA* 3.1 30.8 + - - +
147B ALA* 5.0 0.2 - - - -
318B ILE* 3.4 15.7 - - - +
319B GLY* 5.4 0.2 - - - -
331B ALA* 3.3 31.5 - - - +
332B GLU* 4.2 0.2 - - - -
335B GLY* 4.0 2.3 - - - -
480B FAD 2.9 15.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 18 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.6 12.3 - - - +
13B GLY 3.1 23.6 - - - -
15B GLY 3.0 6.7 + - - -
17B GLY* 1.3 73.9 - - - +
19B TYR* 1.3 58.9 + - - -
21B ALA* 3.3 3.7 + - - +
22B ALA* 2.9 25.3 + - - +
147B ALA* 3.6 21.5 - - - +
480B FAD 3.9 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 19 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452A HIS* 6.1 0.7 - - - -
472A ILE* 4.9 0.7 - - + -
473A ASN* 2.6 32.6 + - - -
13B GLY 3.8 2.6 + - - -
14B SER* 3.6 14.1 - - - +
15B GLY 2.8 28.6 + - - -
16B PRO* 4.0 12.3 - - + -
18B GLY* 1.3 69.9 - - - -
20B VAL* 1.3 86.5 + - + +
22B ALA 3.4 0.2 + - - -
23B ILE* 3.1 51.3 + - + +
42B GLY* 5.1 1.6 - - - -
46B LEU* 5.8 3.1 - - + -
103B ILE* 3.7 44.7 - - + +
106B LEU* 4.7 2.2 - - + -
107B PHE* 3.5 25.8 - - + -
332B GLU* 4.3 7.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 20 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 4.2 18.7 - - + +
473A ASN* 5.2 0.9 - - - +
16B PRO 3.2 20.9 + - - +
17B GLY 4.1 0.9 - - - +
18B GLY 3.3 0.6 - - - -
19B TYR* 1.3 104.7 - - + +
21B ALA* 1.3 57.1 + - - +
23B ILE* 3.5 5.8 + - - +
24B LYS* 3.0 27.2 + - - +
332B GLU* 3.8 33.0 - - + +
336B ILE* 3.5 33.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 21 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 4.8 0.7 - - + -
17B GLY 3.1 20.5 + - - +
18B GLY 3.5 4.7 - - - +
20B VAL* 1.3 75.3 - - - +
22B ALA* 1.3 60.0 + - - +
24B LYS* 3.4 2.5 + - - +
25B ALA* 2.8 34.0 + - - +
145B LEU* 3.5 32.1 - - + -
335B GLY* 3.8 23.5 - - - +
339B VAL* 3.9 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B VAL* 3.8 19.4 - - + +
18B GLY 2.9 17.3 + - - +
19B TYR 3.6 6.1 - - - +
21B ALA* 1.3 75.9 - - - +
23B ILE* 1.3 62.4 + - - +
25B ALA* 3.6 2.6 - - - +
26B ALA* 3.0 23.9 + - - +
32B THR* 3.6 13.7 - - + +
107B PHE* 3.7 20.6 - - + -
112B VAL* 3.8 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A ILE* 3.8 27.1 - - + +
19B TYR* 3.1 41.9 + - + +
20B VAL* 3.7 4.5 - - - +
22B ALA* 1.3 75.6 - - - +
24B LYS* 1.3 58.0 + - - +
26B ALA* 3.2 4.6 + - - +
27B GLN* 2.9 48.2 + - - +
106B LEU* 3.8 25.8 - - + +
107B PHE* 3.8 16.8 - - + -
110B ASN* 3.5 23.5 - - - +
112B VAL* 4.1 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A LEU* 4.4 14.6 - - - +
468A PHE* 3.7 36.8 - - - -
472A ILE* 3.7 20.9 - - + +
20B VAL 3.0 17.8 + - - +
21B ALA* 3.9 4.3 - - - +
23B ILE* 1.3 76.8 - - - +
25B ALA* 1.3 59.6 + - - +
27B GLN* 3.4 11.7 + - + +
28B LEU* 2.9 44.1 + - + +
336B ILE* 4.2 24.1 - - + +
339B VAL* 3.8 17.7 - - + -
340B GLU* 3.6 27.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B VAL* 4.5 8.5 - - + -
21B ALA 2.8 22.2 + - - +
22B ALA 3.6 4.0 - - - +
24B LYS* 1.3 69.6 - - - +
26B ALA* 1.3 66.3 + - - +
28B LEU* 3.0 13.0 + - - +
29B GLY 3.2 0.9 + - - -
30B PHE* 3.0 38.2 + - + -
32B THR* 3.7 16.2 - - + +
339B VAL* 3.8 19.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B ALA 3.0 13.9 + - - +
23B ILE 3.4 8.5 - - - +
25B ALA* 1.3 77.0 - - - +
27B GLN* 1.3 61.1 + - - +
29B GLY* 3.1 14.7 + - - -
30B PHE 3.7 9.3 + - - +
32B THR* 3.4 12.0 + - - +
110B ASN* 3.4 28.5 - - + +
111B LYS 5.2 0.4 - - - -
112B VAL* 3.7 13.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 27 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PHE* 3.7 35.5 - - + -
470A LYS* 3.7 32.2 - - + +
471A SER 3.3 22.8 + - - +
472A ILE* 4.1 8.0 - - - +
474A PHE 5.3 1.6 + - - -
23B ILE* 2.9 39.9 + - - +
24B LYS* 3.7 18.4 - - - +
26B ALA* 1.3 75.4 - - - +
28B LEU* 1.3 59.3 - - - +
29B GLY 3.4 0.4 + - - -
109B GLN* 5.6 1.0 - - - +
110B ASN* 3.3 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A PHE* 4.3 22.9 - - + -
24B LYS* 2.9 32.9 + - + +
25B ALA* 3.0 11.3 + - - +
27B GLN* 1.3 79.5 - - - +
29B GLY* 1.3 56.2 + - - +
30B PHE* 4.2 10.0 - - + -
339B VAL* 3.5 41.5 - - + +
340B GLU* 3.9 12.3 - - + -
343B ALA* 4.3 15.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 29 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B ASP* 4.8 2.4 - - - +
26B ALA 3.1 10.2 + - - -
27B GLN 3.4 1.2 + - - -
28B LEU* 1.3 79.3 - - - +
30B PHE* 1.3 66.7 + - - +
31B LYS 4.1 0.5 + - - -
----------------------------------------------------------
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