Contacts of the helix formed by residues 108 - 124 (chain A) in PDB entry 1ND4
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 ALA 108 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106A HIS 3.7 1.8 + - - -
107A LEU* 1.3 77.6 - - - +
109A PRO* 1.3 77.6 - - + +
110A ALA* 3.3 2.7 - - + +
111A GLU* 3.0 33.2 + - - +
112A LYS* 3.0 11.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 109 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU 3.9 1.3 - - - +
108A ALA* 1.3 87.6 - - + +
110A ALA* 1.3 63.2 + - - +
112A LYS* 3.0 10.1 + - + +
113A VAL* 2.9 27.5 + - - +
232A LEU* 4.3 24.0 - - + +
236A TRP* 3.5 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A ALA* 3.3 1.9 - - + +
109A PRO* 1.3 79.9 - - - +
111A GLU* 1.3 74.1 + - - +
113A VAL* 3.4 5.5 - - - +
114A SER* 3.2 24.3 + - - -
236A TRP* 3.7 27.6 - - + -
243A LEU* 5.0 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A LEU* 4.1 23.8 - - + -
108A ALA* 3.0 31.9 + - - +
110A ALA* 1.3 85.0 - - - +
112A LYS* 1.3 60.7 + - - +
114A SER* 3.2 5.6 + - - -
115A ILE* 2.9 42.4 + - + +
201A GLY* 5.9 2.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 112 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 2.9 52.1 + - + +
103A LEU* 3.1 14.3 + - - +
105A SER* 2.9 32.6 + - - -
107A LEU* 3.3 22.2 + - + +
108A ALA 3.0 14.9 + - - +
109A PRO* 3.0 9.0 + - + +
111A GLU* 1.3 76.6 - - - +
113A VAL* 1.3 58.4 + - - +
115A ILE 3.2 1.4 + - - -
116A MET* 2.9 30.0 + - - +
193A LEU* 5.1 8.5 - - + +
232A LEU* 4.4 28.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO 2.9 18.8 + - - +
110A ALA* 3.4 18.4 - - - +
112A LYS* 1.3 71.7 - - - +
114A SER* 1.3 59.9 + - - +
116A MET* 3.7 7.5 - - - +
117A ALA* 2.9 29.6 + - - +
228A ILE* 4.1 12.6 - - + -
232A LEU* 4.0 20.4 - - + -
236A TRP* 3.6 35.7 - - + +
239A ARG* 4.2 5.8 - - + -
240A PHE* 3.8 14.5 - - + -
243A LEU* 3.9 17.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 114 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A ALA 3.2 16.6 + - - -
111A GLU* 3.2 6.9 + - - -
112A LYS 3.2 0.6 - - - -
113A VAL* 1.3 80.6 - - - +
115A ILE* 1.3 61.0 + - - +
117A ALA* 3.4 2.7 + - - +
118A ASP* 2.8 44.3 + - - +
243A LEU* 4.1 17.3 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 115 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 4.2 20.0 - - + -
107A LEU* 3.4 32.8 - - + -
111A GLU* 2.9 27.6 + - + +
112A LYS 3.6 3.1 - - - +
114A SER* 1.3 73.9 - - - +
116A MET* 1.3 61.2 + - - +
118A ASP* 3.2 11.1 + - - +
119A ALA* 2.9 28.6 + - - +
196A ILE* 4.3 8.1 - - + -
198A VAL* 3.8 8.5 - - + -
201A GLY 3.8 21.3 - - - +
202A ARG* 4.6 0.9 - - - -
203A PHE* 3.9 31.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 116 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A LEU* 3.9 15.2 - - + +
112A LYS 2.9 17.3 + - - +
113A VAL* 3.7 7.2 - - - +
115A ILE* 1.3 78.4 - - - +
117A ALA* 1.3 60.9 + - - +
119A ALA* 3.3 4.1 + - - +
120A MET* 3.0 35.6 + - + +
191A ALA* 3.4 32.5 - - + +
192A CYS 3.9 6.7 - - - +
193A LEU* 4.0 9.6 - - + +
196A ILE* 3.6 37.7 - - + -
224A ALA* 3.9 11.7 - - + +
228A ILE* 4.0 15.3 - - + -
240A PHE* 3.7 19.7 - - + -
----------------------------------------------------------
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 VAL 2.9 18.5 + - - +
114A SER* 3.7 4.0 - - - +
116A MET* 1.3 76.0 - - - +
118A ASP* 1.3 57.8 + - - +
120A MET* 3.5 1.8 + - - +
121A ARG* 2.9 53.1 + - - +
240A PHE* 3.6 14.7 - - + -
243A LEU* 3.8 22.4 - - + -
244A TYR* 3.8 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114A SER* 2.8 37.0 + - - +
115A ILE* 3.2 13.4 + - - +
117A ALA* 1.3 76.3 - - - +
119A ALA* 1.3 61.5 + - - +
121A ARG* 3.0 28.9 + - - +
122A ARG* 3.1 26.6 + - - +
203A PHE* 5.2 9.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ILE 2.9 16.3 + - - +
116A MET 3.6 4.5 - - - +
118A ASP* 1.3 78.5 - - - +
120A MET* 1.3 63.7 + - + +
122A ARG* 3.4 4.7 + - - +
123A LEU 3.1 18.5 + - - -
196A ILE* 4.2 10.1 - - + -
203A PHE* 3.8 31.6 - - + -
206A PHE* 3.6 30.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A MET* 3.0 34.5 + - + +
117A ALA 3.9 0.4 - - - +
119A ALA* 1.3 75.8 - - + +
121A ARG* 1.3 58.8 + - - +
123A LEU* 3.4 3.2 + - + -
124A HIS* 2.8 38.9 + - - +
188A HIS* 4.7 4.3 - - + -
191A ALA* 3.9 19.1 - - + -
196A ILE* 4.5 1.8 - - + -
206A PHE* 3.7 28.9 - - + -
220A ASP* 3.8 37.9 - - - +
221A ILE* 4.9 1.6 - - + -
224A ALA* 5.0 0.7 - - - -
240A PHE* 3.9 18.4 - - + -
244A TYR* 3.7 24.0 - - + -
----------------------------------------------------------
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 43.0 + - - +
118A ASP* 3.0 28.9 + - - +
120A MET* 1.3 75.5 - - - +
122A ARG* 1.3 57.5 + - - +
124A HIS* 3.3 3.3 + - - +
125A THR* 2.7 35.5 + - - +
243A LEU* 3.1 22.4 + - - +
244A TYR* 3.4 38.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A GLY 3.1 29.1 + - - -
75A VAL* 4.2 15.7 - - + +
76A PRO* 3.7 22.4 - - - +
118A ASP 3.1 16.9 + - - +
119A ALA* 3.6 4.5 - - - +
120A MET 3.2 0.2 - - - -
121A ARG* 1.3 79.3 - - - +
123A LEU* 1.3 64.2 + - - +
125A THR* 3.1 20.6 + - - -
126A LEU* 3.7 9.6 + - + +
203A PHE* 4.2 22.6 + - - -
206A PHE* 6.2 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 4.1 23.8 - - + -
75A VAL* 4.8 3.6 - - + -
119A ALA 3.1 16.6 + - - +
120A MET* 3.9 5.2 - - + +
122A ARG* 1.3 77.5 - - - +
124A HIS* 1.3 60.8 + - + +
125A THR 3.1 4.9 + - - -
126A LEU* 3.2 26.7 + - + +
186A VAL* 3.5 33.8 - - + +
187A THR 3.9 1.1 - - - -
188A HIS* 3.3 44.0 - - + +
206A PHE* 4.1 25.8 - - + -
212A LEU* 4.7 5.8 - - + -
220A ASP* 4.1 5.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120A MET* 2.8 25.1 + - - +
121A ARG* 3.6 5.6 - - - +
123A LEU* 1.3 77.5 - - + +
125A THR* 1.3 58.8 + - - +
126A LEU 3.5 3.8 - - - +
185A VAL* 3.8 25.0 - - + +
186A VAL 3.1 18.4 + - - -
187A THR* 4.1 6.5 - - + -
217A ARG* 3.8 25.5 + - + +
220A ASP* 2.8 45.4 + - + +
221A ILE* 4.5 1.4 - - - +
244A TYR* 2.7 41.8 - + - +
----------------------------------------------------------
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