Contacts of the helix formed by residues 12 - 25 (chain C) in PDB entry 3UF2
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 12 (chain C).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A GLN* 5.3 2.2 - - - +
10C MET 3.5 3.8 + - - -
11C ILE* 1.3 74.7 - - - +
13C SER* 1.3 65.9 + - - -
14C GLY* 3.0 4.3 - - - -
15C HIS* 3.0 32.8 + - - +
16C LEU* 3.7 8.0 + - - +
125C LYS* 4.1 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 13 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLY* 1.3 71.4 - - - -
14C GLY* 1.3 57.6 + - - +
16C LEU* 3.3 9.6 + - - +
17C GLN* 3.0 51.4 + - - +
125C LYS* 4.1 17.9 + - - +
144F ALA* 5.2 12.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 14 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C GLY* 3.0 2.4 - - - -
13C SER* 1.3 79.8 - - - +
15C HIS* 1.3 62.0 + - - +
17C GLN* 3.5 12.7 + - - +
18C SER* 3.3 24.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 15 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A SER 6.1 0.7 - - - -
32A GLN* 3.4 25.8 + - - -
107A TYR* 5.6 0.6 - - - -
10C MET 4.0 1.6 - - - -
11C ILE* 4.3 10.8 - - + -
12C GLY* 3.0 33.4 + - - +
14C GLY* 1.3 77.8 + - - +
16C LEU* 1.3 60.8 + - + +
18C SER* 3.0 18.5 + - - -
19C LEU* 3.2 19.1 + - - +
79C GLN* 4.3 20.3 + - + +
80C LEU* 3.7 24.5 - - + +
83C LEU* 3.5 35.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.1 10.5 - - + -
12C GLY 4.0 9.2 - - - +
13C SER* 3.3 8.2 + - - +
14C GLY 3.3 0.4 - - - -
15C HIS* 1.3 79.8 - - + +
17C GLN* 1.3 65.4 + - + +
19C LEU* 3.3 12.0 + - + +
20C GLN* 3.1 22.0 + - - +
118C LYS* 5.1 2.4 - - + +
121C PHE* 3.9 34.1 - - + -
122C ASN* 3.6 33.7 - - + +
125C LYS* 3.7 26.9 - - + -
126C ASN* 5.6 1.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C SER* 3.0 39.6 + - - +
14C GLY* 3.9 9.4 - - - +
15C HIS 3.4 0.2 - - - -
16C LEU* 1.3 78.8 - - + +
18C SER* 1.3 55.8 + - - +
20C GLN* 3.4 7.8 + - - +
21C ARG* 3.1 40.6 + - - +
100F LYS* 3.8 14.8 + - - +
101F ALA* 3.4 41.8 + - - +
143F PHE 5.5 1.8 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 18 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C GLY 3.3 11.4 + - - -
15C HIS* 3.0 17.7 + - - -
17C GLN* 1.3 76.7 - - - +
19C LEU* 1.3 59.0 + - - +
20C GLN 3.2 0.2 - - - -
21C ARG* 3.7 22.9 - - - +
22C LEU* 2.8 31.0 + - - +
73C ASN* 5.1 0.9 - - - +
76C ALA* 4.2 27.9 + - - +
79C GLN* 5.4 3.8 + - - -
80C LEU* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 19 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C HIS 3.2 14.5 + - - +
16C LEU* 3.3 19.0 + - + +
18C SER* 1.3 81.6 + - - +
20C GLN* 1.3 57.7 + - - +
22C LEU* 3.2 20.0 - - + +
23C ILE* 3.0 33.5 + - + +
65C MET* 5.1 2.5 - - + -
80C LEU* 3.8 25.3 - - + +
114C LEU* 5.1 2.7 - - + +
117C VAL* 4.0 22.9 - - + -
118C LYS* 4.1 22.7 - - + +
121C PHE* 3.9 35.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LEU 3.1 11.6 + - - +
17C GLN* 3.5 10.8 - - - +
18C SER 3.2 0.2 - - - -
19C LEU* 1.3 75.3 - - - +
21C ARG* 1.3 54.2 + - - +
22C LEU 3.0 1.1 - - - -
23C ILE* 2.8 22.5 + - - +
24C ASP* 2.6 68.4 + - - +
115C GLU* 5.7 1.0 + - - -
118C LYS* 3.0 35.5 + - + +
68D ARG* 4.9 5.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 21 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN* 3.1 32.0 + - - +
18C SER* 3.4 19.9 + - - +
20C GLN* 1.3 75.6 - - - +
22C LEU* 1.3 58.6 + - - +
24C ASP* 3.8 12.4 + - + +
25C SER* 2.8 31.9 + - - -
72C PRO* 6.2 5.1 - - - +
73C ASN* 4.3 4.8 - - - +
21D ARG* 6.4 0.4 - - - +
72D PRO* 6.4 3.8 - - + -
100F LYS* 3.1 50.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER 2.8 16.8 + - - +
19C LEU* 3.2 19.3 - - + +
21C ARG* 1.3 78.1 - - - +
23C ILE* 1.3 58.7 + - - +
25C SER* 3.0 14.2 + - - -
26C GLN* 3.3 20.1 + - - +
65C MET* 3.9 12.8 - - + -
67C PHE* 3.7 24.5 - - + -
73C ASN* 3.6 43.9 + - + +
76C ALA* 4.3 8.1 - - + -
77C ILE* 4.0 8.7 - - + -
80C LEU* 6.2 0.7 - - + -
114C LEU* 3.4 38.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C LEU* 3.0 18.7 + - + +
20C GLN* 2.8 20.5 + - - +
22C LEU* 1.3 75.7 - - + +
24C ASP* 1.3 63.9 + - - +
25C SER 3.3 0.3 + - - -
26C GLN* 3.4 16.3 + - - +
111C LEU* 4.0 16.7 - - + +
114C LEU* 3.6 38.1 - - + +
115C GLU* 4.3 15.7 - - - +
118C LYS* 3.9 37.0 - - + -
68D ARG* 3.8 23.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 24 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 2.6 54.1 + - - +
21C ARG* 3.8 11.7 + - + +
22C LEU 3.4 0.4 - - - -
23C ILE* 1.3 73.6 - - - +
25C SER* 1.3 58.9 + - - +
26C GLN 3.5 5.5 + - - +
67D PHE* 4.7 2.1 - - - -
68D ARG* 3.2 35.6 + - - +
71D THR* 3.8 37.8 + - + +
72D PRO* 6.2 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 25 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ARG* 2.8 23.4 + - - -
22C LEU 3.0 11.4 + - - -
23C ILE 3.2 0.2 - - - -
24C ASP* 1.3 75.7 - - - +
26C GLN* 1.3 62.0 + - - +
73C ASN* 3.1 18.5 + - - -
25D SER* 3.8 17.7 + - - -
26D GLN* 2.8 23.6 + - - -
67D PHE* 3.6 1.3 - - - -
71D THR* 5.7 1.1 - - - -
72D PRO* 6.5 0.4 - - - -
73D ASN* 3.0 19.9 + - - +
----------------------------------------------------------
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