Contacts of the helix formed by residues 102 - 113 (chain M) in PDB entry 4GUN
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 SER 102 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99M ASP* 2.6 25.7 + - - -
101M SER* 1.4 83.0 + - - +
103M ALA* 1.3 55.3 + - - +
104M LEU 3.8 1.0 + - - -
105M GLY 3.1 12.3 + - - -
106M LYS* 2.8 31.1 + - - +
201M GLU* 3.4 33.9 + - - +
303M SO4 3.5 22.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 103 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101M SER 3.9 0.4 + - - -
102M SER* 1.3 70.1 - - - +
104M LEU* 1.4 61.6 + - - +
106M LYS* 3.5 19.3 + - - +
107M GLN* 3.1 23.7 + - - +
204M TYR* 3.8 25.2 - - + -
205M SER* 3.9 7.2 - - - +
303M SO4 2.8 25.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M PRO* 4.2 11.2 - - + -
102M SER* 3.2 3.4 + - - +
103M ALA* 1.4 74.5 - - - +
105M GLY* 1.3 60.9 + - - +
107M GLN* 3.1 5.2 + - - +
108M ILE* 3.0 48.5 + - + +
137M ILE* 5.5 1.6 - - + -
147M LEU* 4.0 14.8 - - + -
166M ILE* 3.9 15.9 - - + -
197M TRP* 4.3 4.0 - - + -
200M ALA* 3.5 38.6 - - + -
201M GLU* 3.6 19.1 - - + +
204M TYR* 3.7 38.2 - - + -
205M SER* 5.1 0.4 + - - -
303M SO4 4.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 105 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M PRO* 4.7 7.1 - - - +
99M ASP 3.3 22.0 - - - -
100M THR* 3.6 11.7 - - - +
102M SER* 3.1 9.9 + - - -
104M LEU* 1.3 76.3 - - - +
106M LYS* 1.3 59.5 + - - +
108M ILE* 3.6 11.3 + - - +
109M VAL* 3.3 29.6 + - - +
115M VAL* 6.3 0.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 106 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M THR 3.3 17.2 + - - +
101M SER* 3.5 20.2 - - - +
102M SER 2.8 17.5 + - - +
103M ALA* 3.6 18.5 + - - +
105M GLY* 1.3 70.9 - - - -
107M GLN* 1.3 58.7 + - - +
109M VAL* 3.5 5.6 + - - +
110M ALA* 3.0 28.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 107 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103M ALA 3.1 12.7 + - - +
104M LEU 3.1 9.2 + - - +
106M LYS* 1.3 73.7 - - - +
108M ILE* 1.4 58.0 + - - +
110M ALA* 3.4 7.9 + - - +
111M GLN* 2.9 73.8 + - - +
144M GLY 4.3 8.7 + - - +
145M GLY 3.6 10.9 + - - +
146M ALA* 4.1 4.9 - - - +
147M LEU* 4.0 11.9 - - + -
204M TYR* 3.1 27.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98M PRO* 3.7 29.8 - - + -
104M LEU* 3.0 34.9 + - + +
105M GLY* 3.8 5.4 - - - +
106M LYS 3.5 0.2 - - - -
107M GLN* 1.4 72.7 - - - +
109M VAL* 1.3 57.3 + - + +
112M TYR* 2.7 34.7 + - + -
113M GLY 3.3 4.3 + - - -
114M SER 3.7 6.7 - - - +
115M VAL* 3.7 38.1 - - + +
118M LEU* 4.0 23.8 - - + -
147M LEU* 3.7 20.2 - - + +
197M TRP* 4.3 7.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 109 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100M THR* 3.8 26.9 - - + +
105M GLY 3.3 18.7 + - - +
106M LYS* 3.8 5.6 - - - +
108M ILE* 1.3 78.8 - - + +
110M ALA* 1.3 64.1 + - - +
113M GLY* 3.0 43.0 + - - +
114M SER* 5.3 2.2 - - - -
115M VAL* 6.1 1.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106M LYS 3.0 18.9 + - - +
107M GLN* 3.7 11.4 - - - +
109M VAL* 1.3 77.8 - - - +
111M GLN* 1.4 62.1 + - + +
113M GLY 4.9 0.2 + - - -
144O GLY* 5.5 2.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 111 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107M GLN* 2.9 47.9 + - - +
110M ALA* 1.4 80.0 - - + +
112M TYR* 1.4 68.0 + - + +
113M GLY 3.8 0.2 - - - -
146M ALA* 3.4 8.6 - - - +
147M LEU* 2.8 48.3 + - - +
142O GLN 3.9 2.1 - - - +
143O ASN* 3.0 51.4 + - - +
144O GLY* 3.3 6.9 + - - -
146O ALA* 4.2 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 112 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M ILE* 2.7 28.1 + - - +
111M GLN* 1.4 80.6 - - + +
113M GLY* 1.3 54.9 + - - +
114M SER 3.2 20.6 + - - +
117M ASN* 3.0 27.1 + - - +
118M LEU* 3.6 37.3 - - + +
121M ILE* 3.5 35.7 - - + -
147M LEU* 3.2 44.6 + - + +
148M ASP* 3.5 13.2 + - - -
149M VAL* 4.2 1.7 + - - +
142O GLN* 3.7 9.2 - - + -
143O ASN* 3.5 23.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 113 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108M ILE 3.3 1.2 + - - -
109M VAL* 3.0 39.1 + - - +
111M GLN 3.8 0.6 - - - -
112M TYR* 1.3 73.7 - - - +
114M SER* 1.4 59.2 + - - +
----------------------------------------------------------
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