Contacts of the helix formed by residues 113 - 124 (chain A) in PDB entry 1H5Y
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
----------------------------------------------------------
109A ALA* 2.9 16.8 - - - +
110A VAL 3.9 1.8 - - - +
111A ARG 3.8 5.8 - - - +
112A ASN* 1.3 89.5 - - - +
114A GLN* 1.3 58.0 + - + +
116A VAL* 3.0 30.4 + - + +
117A ALA 4.0 0.2 + - - -
159A TRP* 3.9 9.9 - - + -
162A GLU* 4.0 11.4 - - - +
166A LEU* 3.4 25.5 - - + +
6B ARG* 6.5 1.1 - - - -
126B GLN* 3.9 23.3 - - + +
200B PRO* 5.5 2.5 - - + -
222B ASP* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A ASN* 3.1 9.0 + - - +
113A PRO* 1.3 75.5 - - + +
115A LEU* 1.3 66.1 + - - +
116A VAL 3.1 0.2 - - - -
117A ALA* 2.9 19.3 + - + +
118A LEU* 3.1 16.0 + - + +
166A LEU* 4.5 11.7 - - + -
4B ALA* 3.4 26.3 + - + +
5B LEU 3.2 24.8 + - - +
6B ARG* 3.9 22.9 - - + +
222B ASP* 2.8 51.5 + - - +
250B GLU* 4.1 4.5 - - - +
251B VAL* 5.5 0.3 - - - -
----------------------------------------------------------
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
----------------------------------------------------------
88A SER* 4.2 10.5 - - - -
89A LEU* 3.6 39.3 - - + +
105A VAL* 4.1 17.5 - - + -
108A ALA* 3.8 36.3 - - + +
109A ALA* 4.3 2.5 - - - +
112A ASN* 3.0 28.7 + - + +
114A GLN* 1.3 79.2 - - - +
116A VAL* 1.3 56.0 + - - +
118A LEU* 3.2 11.6 + - + +
119A LEU* 2.9 42.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A VAL* 4.2 5.8 - - + -
109A ALA* 3.8 22.0 - - + -
113A PRO* 3.0 16.9 + - + +
115A LEU* 1.3 75.8 - - - +
117A ALA* 1.3 59.9 + - - +
119A LEU* 3.3 9.7 + - - +
120A ALA* 2.9 27.5 + - - +
128A THR* 4.0 5.6 - - + +
130A VAL* 3.8 21.8 - - + -
163A VAL* 3.8 12.3 - - + +
166A LEU* 3.8 17.0 - - + -
168A ALA* 3.6 36.8 - - + +
----------------------------------------------------------
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
----------------------------------------------------------
113A PRO 4.0 0.4 + - - -
114A GLN* 2.9 15.2 + - + +
116A VAL* 1.3 80.7 - - - +
118A LEU* 1.3 55.9 + - - +
120A ALA* 3.4 2.4 + - - +
121A ARG* 2.9 30.5 + - - +
166A LEU* 3.3 35.3 + - + +
250B GLU* 4.1 25.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.4 24.1 - - + +
112A ASN* 5.8 2.5 - - - +
114A GLN* 3.1 12.7 + - + +
115A LEU* 3.2 17.2 + - + +
117A ALA* 1.3 72.6 - - - +
119A LEU* 1.3 66.2 + - - +
121A ARG* 3.7 7.6 - - + +
122A GLU* 3.0 26.5 + - - +
2B HIS* 3.6 35.4 - - - +
3B MET 3.8 15.7 - - - +
4B ALA* 3.9 18.6 - - + -
250B GLU* 4.0 13.5 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
89A LEU* 3.8 16.2 - - + -
92A ALA* 3.5 29.2 - - + -
96A PHE* 4.7 5.8 - - + -
103A VAL* 5.4 4.9 - - + +
105A VAL* 3.7 41.1 - - + -
115A LEU* 2.9 30.6 + - + +
116A VAL* 3.6 4.3 - - - +
118A LEU* 1.3 78.6 - - - +
120A ALA* 1.3 56.9 + - - +
123A PHE* 2.8 45.1 + - + +
124A GLY 3.6 0.7 + - - -
128A THR* 3.4 24.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL 2.9 16.1 + - - +
117A ALA* 3.8 4.7 - - - +
119A LEU* 1.3 77.3 - - - +
121A ARG* 1.3 59.1 + - - +
124A GLY* 2.8 30.4 + - - -
125A SER* 3.7 8.4 + - - +
128A THR* 3.4 9.6 + - - +
166A LEU 4.6 0.4 - - - +
167A GLY* 3.5 33.9 - - - +
----------------------------------------------------------
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 ALA 2.9 17.7 + - - +
118A LEU* 3.7 10.1 - - + +
119A LEU 3.2 0.2 - - - -
120A ALA* 1.3 78.6 - - - +
122A GLU* 1.3 62.7 + - + +
124A GLY 4.4 0.9 + - - -
245B LYS* 4.1 25.0 - - - +
250B GLU* 2.5 41.7 + - + +
251B VAL 5.2 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 5.4 4.9 - - + -
93A THR* 5.3 4.7 + - - +
118A LEU 3.0 17.7 + - - +
121A ARG* 1.3 80.5 - - + +
123A PHE* 1.3 94.0 + - + +
124A GLY 3.7 0.2 - - - -
2B HIS* 4.4 25.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89A LEU* 4.7 4.0 - - + -
93A THR* 3.7 34.8 - - + -
96A PHE* 3.4 63.7 - + + -
119A LEU* 2.8 30.1 + - + +
122A GLU* 1.3 106.9 - - + +
124A GLY* 1.3 61.4 + - - +
126A GLN* 2.7 18.5 + - - +
127A SER* 3.3 6.2 + - - -
128A THR* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A LEU 3.6 0.6 + - - -
120A ALA 2.8 17.8 + - - -
121A ARG 4.4 1.0 + - - -
122A GLU 3.7 0.8 - - - -
123A PHE* 1.3 80.8 - - - +
125A SER* 1.3 66.6 + - - -
126A GLN* 3.1 14.1 - - - -
127A SER* 2.9 10.4 + - - -
128A THR* 2.9 16.6 + - - -
----------------------------------------------------------
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