Contacts of the helix formed by residues 10 - 25 (chain A) in PDB entry 3D87
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 10 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 1.3 72.6 - - - +
11A TRP* 1.3 51.5 - - - +
12A THR* 3.0 4.9 - - - -
13A GLN* 2.5 55.6 + - + +
14A CYS* 2.5 20.8 + - - -
115A LEU* 4.2 12.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 11 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A SER* 3.8 18.5 + - - -
9A PRO* 2.9 39.1 + - + -
10A ALA* 1.3 71.1 - - - +
12A THR* 1.3 54.8 + - - +
14A CYS* 3.4 3.6 - - - +
15A GLN* 2.3 39.5 + - - +
63A LEU* 5.3 2.7 - - + -
67A SER* 4.8 12.6 - - - -
71A LEU* 4.2 22.7 - - + -
160A VAL* 3.8 9.0 - - + -
161A PHE* 3.4 54.0 - + - +
164A GLY* 3.8 14.4 - - - -
165A ALA* 3.2 29.0 - - - +
168A LEU* 3.3 39.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 12 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 2.8 3.2 + - - -
11A TRP* 1.3 73.4 + - - +
13A GLN* 1.3 66.0 + - - +
15A GLN* 3.6 6.4 - - + +
16A GLN* 3.0 34.8 + - - +
165A ALA* 4.2 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 13 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA* 2.5 35.1 + - + +
12A THR* 1.3 74.9 - - - +
14A CYS* 1.3 54.9 + - - +
16A GLN* 2.8 24.9 + - - +
17A LEU* 2.8 54.2 + - - +
115A LEU* 3.6 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 14 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 4.2 11.0 - - - -
10A ALA 2.5 17.8 + - - +
11A TRP* 3.4 7.2 - - - +
13A GLN* 1.3 71.9 - - - +
15A GLN* 1.3 53.3 + - - +
17A LEU* 3.6 5.3 - - - +
18A SER* 2.2 44.4 + - - -
112A LEU* 3.8 16.2 - - + +
115A LEU* 3.5 28.9 - - - -
116A LEU* 4.5 3.8 - - - -
161A PHE* 3.4 33.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 15 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A TRP 2.3 31.1 + - - +
12A THR* 3.3 7.2 + - + +
14A CYS* 1.3 67.5 - - - +
16A GLN* 1.3 58.7 + - - +
18A SER* 3.5 2.5 + - - -
19A GLN* 2.6 53.9 + - - +
158A ALA* 3.0 15.0 + - - +
161A PHE* 3.7 4.4 - - - +
162A ALA* 2.8 54.2 - - + +
165A ALA* 3.8 12.3 - - + -
292B TYR* 3.9 2.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 16 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A THR* 3.0 19.4 + - - +
13A GLN* 2.8 38.8 + - - +
15A GLN* 1.3 78.1 - - - +
17A LEU* 1.3 83.6 + - + +
19A GLN* 3.7 7.3 - - - +
20A LYS* 3.1 23.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 17 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A GLN* 2.8 25.0 + - - +
14A CYS* 3.0 5.6 + - - +
16A GLN* 1.3 89.6 - - + +
18A SER* 1.3 62.6 + - - +
20A LYS* 3.6 21.8 + - + +
21A LEU* 3.5 17.7 + - - +
108A SER* 4.3 21.5 - - - +
111A GLY* 5.2 3.6 - - - -
112A LEU* 4.2 17.0 - - + +
115A LEU* 3.2 33.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A CYS 2.2 38.0 + - - -
15A GLN* 3.2 6.1 + - - -
17A LEU* 1.3 70.1 - - - +
19A GLN* 1.3 55.4 + - - +
21A LEU* 2.4 47.3 + - - +
22A CYS* 3.2 3.6 + - - -
112A LEU* 4.1 7.1 - - - +
154A VAL* 5.1 1.1 - - - -
157A ALA* 4.5 2.0 - - - -
158A ALA* 3.7 27.1 - - - -
161A PHE* 3.0 24.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 19 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A GLN* 2.6 46.1 + - - +
16A GLN* 3.7 9.0 - - - +
17A LEU 3.5 0.2 - - - -
18A SER* 1.3 72.1 - - - +
20A LYS* 1.3 62.6 + - - +
21A LEU 3.2 0.5 + - - -
22A CYS* 3.2 19.5 + - - +
23A THR* 3.2 14.3 + - - +
158A ALA* 4.4 3.7 - - - +
270B ASP* 3.5 13.1 + - - -
291B ARG* 3.1 36.7 + - - +
292B TYR* 3.1 19.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 20 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A GLN 3.1 10.2 + - - +
17A LEU* 3.6 18.6 - - + +
18A SER 2.9 1.0 + - - -
19A GLN* 1.3 79.0 - - - +
21A LEU* 1.3 65.2 + - - +
23A THR* 2.9 20.0 + - - -
24A LEU* 3.1 36.9 + - + +
104A GLN* 4.4 12.9 + - - +
108A SER* 3.5 30.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 21 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU 3.8 6.1 - - - +
18A SER* 2.4 33.6 + - - +
20A LYS* 1.3 71.1 - - - +
22A CYS* 1.3 60.6 + - - +
23A THR 3.1 0.3 + - - -
24A LEU* 3.3 4.5 + - - +
25A ALA* 3.0 27.4 + - - +
78A LEU* 4.3 9.4 - - + -
105A LEU* 4.3 15.0 - - + -
108A SER* 4.4 11.9 - - - +
109A LEU* 3.5 36.6 - - + +
112A LEU* 3.4 38.1 - - + -
154A VAL* 3.9 26.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 22 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A SER 3.2 6.7 + - - -
19A GLN 3.2 6.9 + - - +
21A LEU* 1.3 75.6 - - - +
23A THR* 1.3 58.1 + - - +
25A ALA 3.9 1.1 + - - +
26A TRP* 2.8 32.5 - - - -
154A VAL* 3.5 38.8 - - + -
155A ALA 4.0 0.2 - - - -
158A ALA* 3.5 21.8 - - - -
291B ARG 5.3 1.1 - - - +
292B TYR* 3.2 39.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 23 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A GLN* 3.2 15.2 + - - +
20A LYS* 2.9 10.9 + - - -
22A CYS* 1.3 77.0 - - - +
24A LEU* 1.3 72.9 + - + +
25A ALA 3.0 1.4 + - - -
26A TRP* 3.2 17.5 + - - +
27A SER* 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A LYS* 3.1 39.7 + - + +
21A LEU* 4.0 3.4 - - + +
23A THR* 1.3 84.0 - - + +
25A ALA* 1.3 55.1 + - - +
26A TRP 3.3 1.1 - - - -
27A SER* 2.7 29.0 + - - -
101A PRO* 3.3 16.6 - - + +
102A VAL* 5.9 0.3 - - - +
104A GLN* 3.1 31.2 - - + +
105A LEU* 3.0 52.1 - - + +
108A SER* 4.2 6.7 - - - +
147A LEU* 5.8 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 25 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A LEU 3.0 17.0 + - - +
22A CYS 3.9 2.2 + - - +
23A THR 3.0 0.8 + - - -
24A LEU* 1.3 73.6 - - - +
26A TRP* 1.3 57.7 + - - +
27A SER* 3.3 6.3 + - - -
105A LEU* 4.3 10.1 - - + -
147A LEU* 3.7 14.9 - - + +
150A LEU* 4.1 26.2 - - + -
151A GLN* 2.8 37.5 + - + +
154A VAL* 4.2 10.5 - - + -
----------------------------------------------------------
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