Contacts of the helix formed by residues 117 - 126 (chain A) in PDB entry 1D02
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 ASN 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ARG 4.5 2.2 - - - +
116A GLY* 1.3 73.6 - - - +
118A ALA* 1.3 66.4 + - - +
119A HIS* 3.1 13.9 - - + -
120A GLU* 3.0 39.4 + - - +
162A ARG* 5.4 2.7 - - - +
121B ARG* 3.2 25.2 + - - +
3C C 3.4 23.5 + - + +
4C A 2.9 29.5 + - - -
5C A 2.8 26.2 + - - -
6D T 3.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 5.1 1.5 - - - +
102A GLN* 3.7 9.7 + - - +
117A ASN* 1.3 78.7 - - - +
119A HIS* 1.3 56.6 + - - +
120A GLU 3.0 0.4 - - - -
121A ARG* 2.9 36.2 + - - +
121B ARG* 4.6 4.5 - - - +
5C A 4.3 6.3 - - - +
5D A 3.6 41.1 - - + +
6D T 3.1 23.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A LYS* 4.5 16.8 - - + -
102A GLN* 3.0 26.0 + - + +
116A GLY 3.6 0.4 - - - -
117A ASN* 3.5 21.9 - - + -
118A ALA* 1.3 76.2 - - - +
120A GLU* 1.3 62.2 + - + +
121A ARG 3.0 0.2 - - - -
122A SER* 2.7 31.6 + - - -
152A PHE* 4.3 11.7 - + + -
156A ILE* 3.8 21.5 - - + -
162A ARG* 3.5 28.7 - - - -
165A GLU* 2.8 29.3 + - - -
166A ILE* 4.2 9.6 - - + -
169A TRP* 3.7 25.4 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A ASN* 3.0 31.4 + - + +
119A HIS* 1.3 81.5 - - + +
121A ARG* 1.3 63.6 + - - +
123A CYS* 2.8 22.8 + - - +
165A GLU* 4.3 5.7 - - - +
169A TRP* 3.7 29.2 - - + -
120B GLU 3.9 5.0 - - - +
121B ARG* 3.0 51.6 + - - +
124B LYS* 2.7 37.0 + - + +
3C C 4.2 6.1 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
100A LYS* 3.2 16.7 - - - +
118A ALA* 2.9 20.6 + - - +
120A GLU* 1.3 78.9 - - - +
122A SER* 1.3 61.5 + - - +
123A CYS 3.0 1.2 + - - -
124A LYS* 3.1 28.6 + - - +
117B ASN* 3.2 34.8 - - - +
118B ALA* 4.5 1.8 - - - +
120B GLU* 2.9 40.0 + - + +
121B ARG* 3.9 17.5 - - + +
3D C 3.5 8.7 + - - +
4D A 3.0 33.9 + - - +
5D A 3.0 49.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98A GLU* 5.2 5.4 - - - -
100A LYS* 3.9 32.4 - - - +
119A HIS 2.7 21.8 + - - -
121A ARG* 1.3 78.0 - - - +
123A CYS* 1.3 65.4 + - - +
124A LYS* 3.0 5.6 + - - -
125A LEU* 3.2 24.2 + - - +
126A PHE* 4.9 2.7 - - - -
148A PHE* 5.4 0.2 - - - -
150A VAL* 4.4 24.3 - - - +
152A PHE* 4.4 7.4 - - - -
169A TRP* 5.0 1.4 - - - -
170A TYR* 4.9 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A GLU 2.8 16.4 + - - +
122A SER* 1.3 75.9 - - - +
124A LYS* 1.3 61.6 + - - +
125A LEU 2.9 6.3 - - - -
126A PHE* 2.9 30.3 + - - +
127A THR 4.0 0.9 + - - -
169A TRP* 3.5 35.4 - - - -
170A TYR* 5.8 0.4 - - - -
123B CYS* 3.5 26.3 - - - +
124B LYS* 3.5 11.9 - - - +
127B THR* 3.5 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.7 18.9 - - - +
98A GLU* 6.5 0.9 - - - -
121A ARG* 3.1 14.9 + - - +
122A SER* 3.0 3.9 - - - +
123A CYS* 1.3 77.6 - - - +
125A LEU* 1.3 71.0 + - + +
127A THR* 2.9 29.5 + - - +
130A LEU* 3.3 27.3 - - + +
120B GLU* 2.7 43.8 + - + +
123B CYS* 3.5 26.0 - - - +
165B GLU* 4.4 7.5 + - - -
169B TRP* 4.1 13.9 - - + +
3D C 3.7 18.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 6.1 0.9 - - + -
96A PHE 5.7 0.2 - - - +
97A GLY 5.7 0.2 - - - -
98A GLU* 3.5 36.1 - - + +
122A SER* 3.6 14.4 - - - +
123A CYS 2.9 1.2 - - - -
124A LYS* 1.3 92.1 - - + +
126A PHE* 1.3 55.3 + - - +
127A THR 3.3 2.0 + - - +
130A LEU* 4.4 10.2 - - + +
131A LEU* 3.4 20.1 + - - +
134A TYR* 3.2 37.1 - - + +
148A PHE* 3.4 60.1 - - + -
150A VAL* 4.5 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A SER 4.9 0.9 - - - -
123A CYS* 2.9 27.1 + - - +
125A LEU* 1.3 75.2 - - - +
127A THR* 1.3 67.0 + - - +
128A PRO* 3.4 2.9 - - - +
131A LEU* 3.4 17.7 - - + +
146A LEU* 3.3 30.1 - - + -
148A PHE* 3.7 12.8 - + - -
170A TYR* 3.6 47.6 - + - -
126B PHE* 3.7 28.6 - - + +
127B THR* 3.7 23.8 - - + +
128B PRO* 3.4 32.3 - - + -
----------------------------------------------------------
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