Contacts of the helix formed by residues 113 - 120 (chain A) in PDB entry 4X2Q
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 PRO 113 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A GLY 3.6 4.0 - - - +
112A LYS* 1.4 91.8 - - + +
114A PHE* 1.3 65.2 + - - +
115A LEU* 3.3 2.9 - - + +
116A GLN* 3.1 32.7 + - + +
117A ALA* 3.1 17.0 + - - +
298A GLN* 3.2 17.5 - - - +
334A PRO* 3.6 13.7 - - + +
336A ASP 5.8 0.2 - - - +
339A THR* 4.1 18.4 - - - +
340A GLU 3.4 16.2 - - - +
341A GLN 4.2 1.1 - - - -
342A GLY* 3.9 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO 4.0 12.8 - - - -
10A SER 3.5 11.0 - - - -
11A PRO* 3.4 46.9 - - + -
100A ALA* 3.7 9.2 - - + -
103A ALA* 3.7 18.6 - - + -
104A THR* 3.2 36.8 - - + -
107A SER* 3.2 14.5 + - - +
113A PRO* 1.3 70.5 - - - +
115A LEU* 1.3 69.6 + - + +
117A ALA* 3.1 5.5 + - - +
118A PHE* 2.9 45.8 + + + +
334A PRO 2.8 19.6 + - - +
335A PHE* 4.5 4.7 - + + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A PRO* 4.0 25.4 - - + +
113A PRO* 3.3 2.8 - - + +
114A PHE* 1.3 87.4 - - + +
116A GLN* 1.3 59.5 + - + +
118A PHE* 4.5 2.7 - - + +
119A TYR* 3.0 56.3 + - + +
337A PRO* 3.5 43.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LYS* 3.6 21.5 - - + +
113A PRO* 3.1 26.2 + - + +
115A LEU* 1.3 78.6 - - + +
117A ALA* 1.3 57.4 + - - +
120A VAL* 2.9 40.7 + - + +
121A ASP* 3.0 8.8 + - - +
292A GLN* 5.5 1.2 + - - -
296A PHE* 3.4 34.2 - - - +
297A ASN* 4.2 6.7 - - - +
298A GLN* 4.8 0.7 + - - +
329A ARG* 5.2 2.6 + - - +
339A THR 5.1 0.2 - - - +
340A GLU* 2.9 27.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 117 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A ALA* 3.6 27.6 - - + +
106A GLU* 4.5 14.4 - - + -
107A SER* 4.8 3.4 - - - +
112A LYS* 4.8 6.2 - - + +
113A PRO 3.1 10.7 + - - +
114A PHE* 3.1 12.2 + - - +
116A GLN* 1.3 78.8 - - - +
118A PHE* 1.3 56.9 + - - +
121A ASP* 3.6 13.0 - - + +
122A LEU* 3.0 35.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
9A PRO* 3.8 28.5 - - + -
99A ARG* 3.1 72.9 + - + -
100A ALA* 3.6 34.3 - - + -
103A ALA* 3.9 8.5 - - + -
114A PHE* 2.9 27.4 + + + +
115A LEU* 3.9 6.1 - - + +
116A GLN 3.3 0.2 - - - -
117A ALA* 1.3 79.4 - - - +
119A TYR* 1.3 84.4 + + + +
122A LEU* 4.1 2.6 - - - +
123A GLN 4.1 4.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8A LEU 4.9 2.6 + - - -
9A PRO* 3.4 33.9 - - + +
99A ARG* 4.3 7.4 - - - +
115A LEU* 3.0 37.2 + - + +
118A PHE* 1.3 102.5 - + + +
120A VAL* 1.3 65.0 + - + +
123A GLN* 3.3 35.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A GLN* 2.9 31.2 + - + +
119A TYR* 1.3 84.9 - - + +
121A ASP* 1.3 68.3 + - - +
122A LEU 3.5 0.2 - - - -
123A GLN* 3.5 2.1 + - - +
124A GLY* 3.2 20.1 + - - -
173A LEU* 4.9 3.9 - - + +
296A PHE* 3.6 35.2 - - + -
----------------------------------------------------------
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