Contacts of the helix formed by residues 108 - 122 (chain A) in PDB entry 1MAQ
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 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A SER* 1.3 71.4 + - - +
109A THR* 1.3 54.9 + - - -
111A SER 3.3 1.2 + - - -
112A LEU* 2.9 36.6 + - - +
222A ASP* 5.7 0.7 - - - -
253A SER* 3.2 9.8 + - - -
254A GLN 3.9 6.7 - - - -
255A SER* 3.8 17.1 - - - -
412A PGU 2.8 29.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A ILE 4.7 0.2 - - - -
107A SER 3.5 0.2 - - - -
108A GLY* 1.3 74.2 - - - +
110A GLY* 1.3 58.4 + - - +
112A LEU* 3.4 9.4 - - - +
113A ARG* 2.9 30.4 + - + +
140A TRP* 3.7 6.8 - - - -
142A ASN* 3.8 22.3 + - - +
146A ILE* 3.8 12.3 - - + +
266A ARG* 4.3 7.8 + - - -
412A PGU 2.7 35.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 4.9 0.2 - - - -
106A ILE* 3.1 35.2 + - - -
109A THR* 1.3 79.1 - - - +
111A SER* 1.3 57.6 + - - +
113A ARG* 3.5 4.8 + - - +
114A VAL* 2.8 36.1 + - - +
295A TYR* 6.1 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A GLY* 3.4 14.3 - - - -
106A ILE 4.3 0.4 - - - +
107A SER 2.6 23.3 + - - -
110A GLY* 1.3 75.2 - - - +
112A LEU* 1.3 64.0 + - - +
114A VAL* 3.2 4.3 + - - +
115A GLY 3.0 18.9 + - - -
220A TYR* 4.3 0.4 - - - -
253A SER* 3.2 19.1 - - - -
269A ALA 3.4 34.5 + - - -
270A PHE* 3.6 19.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A GLY 2.9 19.9 + - - +
109A THR* 3.4 6.1 - - - +
111A SER* 1.3 76.2 - - - +
113A ARG* 1.3 58.6 + - - +
116A ALA* 2.9 21.8 + - - +
140A TRP* 3.8 24.0 - - + -
143A HIS* 4.1 7.4 - - + -
146A ILE* 4.1 19.0 - - + +
147A PHE* 4.9 4.7 - - + -
187A LEU* 4.7 7.0 - - + -
220A TYR* 2.9 36.4 + - + +
222A ASP* 3.6 32.5 - - + +
253A SER* 3.5 21.5 + - - -
412A PGU 4.0 6.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 2.9 21.5 + - + +
110A GLY* 3.9 5.6 - - - +
112A LEU* 1.3 74.5 - - - +
114A VAL* 1.3 66.0 + - - +
115A GLY 3.1 1.1 - - - -
116A ALA* 4.4 0.7 - - - +
117A ASN* 2.8 62.0 + - - +
145A PRO 4.9 1.6 + - - -
146A ILE* 3.8 31.7 + - + +
149A ASP* 3.7 44.5 + - - +
150A ALA* 4.0 3.9 - - - +
294A MET* 5.2 9.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A VAL* 5.0 4.0 - - + -
105A GLY* 5.9 1.6 - - - -
110A GLY 2.8 24.5 + - - +
111A SER* 3.7 7.0 - - - +
113A ARG* 1.3 73.1 - - - +
115A GLY* 1.3 58.4 + - - +
117A ASN* 3.5 5.9 + - - +
118A PHE* 2.9 26.3 + - - +
270A PHE* 4.3 11.7 - - + -
287A LEU* 3.7 26.2 - - + -
290A LEU* 4.0 4.9 - - + +
291A ILE* 4.0 30.5 - - + -
294A MET* 4.4 20.4 - - + -
295A TYR* 4.3 13.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER 3.0 9.5 + - - -
114A VAL* 1.3 76.9 - - - +
116A ALA* 1.3 54.3 + - - +
118A PHE* 3.1 3.0 + - - +
119A LEU* 2.8 41.6 + - - +
220A TYR* 3.7 7.2 - - - -
270A PHE* 3.3 36.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU 2.9 16.7 + - - +
113A ARG* 3.3 5.4 + - - +
115A GLY* 1.3 74.4 - - - +
117A ASN* 1.3 51.9 + - - +
119A LEU* 3.2 9.0 + - - +
120A GLN* 2.7 34.0 + - - +
146A ILE* 4.4 6.7 - - + +
147A PHE* 3.6 33.9 - - + -
150A ALA* 3.6 20.0 - - + -
152A LEU* 3.6 5.2 - - + +
220A TYR* 4.1 1.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113A ARG* 2.8 50.7 + - - +
114A VAL* 3.7 5.4 - - - +
116A ALA* 1.3 74.1 - - - +
118A PHE* 1.3 65.0 + - - +
120A GLN* 3.6 9.9 + - - +
121A ARG* 3.2 22.7 + - - +
150A ALA* 3.1 17.8 - - - +
290A LEU* 3.6 21.1 - - + +
294A MET* 4.4 20.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A VAL 2.9 17.5 + - - +
115A GLY* 3.3 7.9 - - - +
117A ASN* 1.3 78.7 - - - +
119A LEU* 1.3 65.7 + - + +
121A ARG* 3.1 2.8 + - - -
122A PHE* 2.7 76.4 + + + +
251A VAL* 5.5 1.8 - - + -
270A PHE* 4.5 13.2 - + - -
272A VAL* 4.4 14.1 - - + -
283A VAL* 3.6 39.7 - - + -
286A GLN* 4.7 4.5 - - + -
287A LEU* 3.8 28.0 - - + -
290A LEU* 3.5 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A GLY* 2.8 16.8 + - - +
116A ALA* 3.3 11.0 - - - +
118A PHE* 1.3 90.0 - - + +
120A GLN* 1.3 61.4 + - - +
123A PHE* 2.7 48.8 + - + +
129A ARG* 3.4 4.5 + - - -
147A PHE* 5.0 2.2 - - + -
152A LEU* 4.1 10.8 - - + -
185A ILE* 4.0 28.3 - - + -
218A LEU* 3.6 24.2 - - + -
220A TYR* 3.9 29.8 - - + -
251A VAL* 5.2 6.7 - - + -
270A PHE* 5.8 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A ALA 2.7 19.5 + - - +
117A ASN* 3.8 8.5 + - - +
119A LEU* 1.3 71.9 - - - +
121A ARG* 1.3 75.5 + - - +
129A ARG* 2.8 36.8 + - - +
150A ALA 3.0 27.6 - - - +
151A GLY* 4.1 14.9 - - - +
152A LEU* 3.9 8.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN 3.2 14.4 + - - +
118A PHE 3.1 4.0 + - - +
119A LEU 3.0 0.4 - - - -
120A GLN* 1.3 93.0 - - - +
122A PHE* 1.3 93.0 + - + +
123A PHE 5.6 0.2 - - - -
286A GLN* 4.9 3.6 + - - +
289A ILE* 3.9 25.7 + - - +
290A LEU* 4.2 30.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A PHE* 2.7 59.6 + + + +
121A ARG* 1.3 107.1 - - + +
123A PHE* 1.3 59.7 + - - +
124A LYS* 3.0 15.1 + - - +
125A PHE* 5.6 1.2 - - - -
286A GLN* 3.5 43.7 - - + -
290A LEU* 5.5 1.1 - - + -
----------------------------------------------------------
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