Contacts of the helix formed by residues 130 - 142 (chain I) in PDB entry 3SDI
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 130 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 3.5 23.5 - - + +
128I GLY 3.2 0.4 - - - -
129I THR* 1.3 75.9 + - - +
131I SER* 1.3 57.7 + - - +
132I ASP 3.3 2.7 - - - -
133I GLN* 3.3 12.9 + - + -
134I LEU* 2.9 28.1 + - - +
162I ALA* 3.9 18.6 - - + +
166I ASP* 2.9 28.0 + - + +
169I SER* 4.4 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 131 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 5.8 2.7 - - - -
126I VAL* 3.9 11.6 - - - +
127I SER* 4.4 5.2 - - - -
128I GLY 3.1 18.9 + - - -
129I THR 3.4 2.3 + - - -
130I ALA* 1.3 77.2 - - - +
132I ASP* 1.3 57.5 + - - +
134I LEU* 3.2 10.7 + - - +
135I PHE* 2.7 46.6 + - - -
201I MG 2.6 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 132 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25H ILE* 3.3 29.7 - - - +
129I THR 5.5 1.9 - - - +
130I ALA 3.3 0.6 - - - -
131I SER* 1.3 79.5 + - - +
133I GLN* 1.3 71.4 + - - +
135I PHE* 3.2 9.3 + - - +
136I GLY 3.0 19.2 + - - -
132Z SER* 3.4 28.2 + - - +
133Z LEU* 3.6 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 133 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129I THR 4.4 3.7 + - - +
130I ALA* 3.3 21.5 + - - +
132I ASP* 1.3 83.5 - - - +
134I LEU* 1.3 58.1 + - - +
136I GLY* 3.3 2.8 + - - -
137I MET* 2.9 31.5 + - - +
162I ALA* 3.5 31.2 - - + +
165I ARG* 3.1 32.4 + - + -
166I ASP* 4.0 10.9 + - - +
24Y ASN 5.4 0.4 + - - -
25Y TRP* 3.7 18.6 - - + +
132Z SER* 3.4 21.7 - - - +
136Z PRO* 3.9 13.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I ILE* 3.9 19.7 - - + -
3I VAL 3.8 14.4 - - - +
4I VAL* 4.0 24.7 - - + -
126I VAL* 3.7 19.7 - - + -
127I SER 3.7 23.6 - - - +
130I ALA 2.9 21.2 + - - +
131I SER* 3.5 4.3 - - - +
133I GLN* 1.3 74.1 - - - +
135I PHE* 1.3 59.5 + - - +
137I MET* 3.4 1.8 + - - +
138I CYS* 2.9 36.3 + - - -
158I ALA* 4.0 13.5 - - + +
159I LEU* 4.1 7.0 - - - -
162I ALA* 3.7 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 135 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22H GLN* 4.0 16.6 - - - -
25H ILE* 3.5 28.9 - - + -
26H VAL 4.0 0.9 - - - -
27H ALA* 3.8 24.9 - - + -
120I ASP* 5.4 3.4 - - - -
124I PHE* 4.0 14.4 - + - -
125I ILE* 6.1 0.2 - - - -
126I VAL* 3.4 29.1 - - + +
131I SER* 2.7 34.9 + - - +
132I ASP* 3.5 8.1 - - - +
134I LEU* 1.3 71.7 - - - +
136I GLY* 1.3 56.8 - - - +
138I CYS* 4.2 2.1 - - - +
139I GLU* 3.0 32.9 + - - +
133Z LEU* 4.7 7.2 - - + -
165Z ARG* 3.2 42.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 136 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132I ASP 3.0 10.3 + - - -
133I GLN 3.6 1.8 - - - -
135I PHE* 1.3 75.2 - - - +
137I MET* 1.3 65.6 + - - +
139I GLU* 3.9 2.7 - - - +
140I SER* 3.1 27.8 + - - -
133Z LEU* 3.2 39.8 - - - +
137Z PHE* 5.4 0.7 - - - -
161Z SER* 4.9 2.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 137 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133I GLN 2.9 22.6 + - - +
134I LEU* 3.8 4.0 - - - +
136I GLY* 1.3 71.5 - - - +
138I CYS* 1.3 52.4 + - - +
140I SER* 3.7 3.1 - - - -
141I LEU* 2.7 72.3 + - + +
158I ALA* 3.6 31.0 - - + +
161I ASN* 3.8 24.9 - - + +
162I ALA* 4.1 4.3 - - + +
133Z LEU 4.1 0.8 + - - -
136Z PRO* 3.5 15.5 - - + +
137Z PHE* 3.3 36.6 - - + -
140Z ASN* 4.2 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 138 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I VAL* 4.0 11.9 - - - -
6I MET* 3.8 25.1 - - + -
124I PHE* 3.5 31.2 - - + -
126I VAL* 3.9 18.4 - - - -
134I LEU* 2.9 26.3 + - - +
137I MET* 1.3 71.2 - - - +
139I GLU* 1.3 67.3 + - - +
141I LEU* 4.4 2.7 - - - +
142I TYR* 2.9 32.8 + - - +
158I ALA* 4.1 8.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29H LYS* 2.8 25.1 + - - -
197H ARG* 3.2 32.5 + - - +
200H LYS* 3.3 17.5 + - - -
124I PHE* 3.7 8.9 - - + -
135I PHE 3.0 21.6 + - - +
136I GLY* 3.9 3.6 - - - +
138I CYS* 1.3 77.5 - - - +
140I SER* 1.3 60.2 + - - +
142I TYR* 4.3 2.1 + - - +
161Z SER* 3.5 22.0 - - - +
164Z GLU* 3.5 5.6 - - + +
165Z ARG* 2.5 46.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 140 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H LYS* 3.2 27.5 - - - +
204H TYR* 3.4 12.6 - - - -
136I GLY 3.1 16.6 + - - -
137I MET 3.7 2.0 - - - -
139I GLU* 1.3 78.3 - - - +
141I LEU* 1.3 60.3 + - - +
133Z LEU 5.4 0.5 + - - -
137Z PHE* 3.5 43.8 - - - +
157Z ASP* 5.0 2.1 + - - -
158Z SER* 5.1 0.5 - - - -
161Z SER* 2.8 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 141 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204H TYR* 3.7 37.0 + - + +
205H LYS 5.0 0.3 + - - -
206H PHE* 3.8 19.2 - - + -
137I MET* 2.7 45.7 + - + +
138I CYS* 4.5 2.2 - - - +
140I SER* 1.3 75.0 - - - +
142I TYR* 1.3 62.8 + - - +
143I GLU* 3.7 8.1 + - - +
154I THR* 3.7 29.3 + - + +
157I GLN* 3.9 11.2 - - + -
158I ALA* 3.6 23.8 - - + +
137Z PHE* 4.5 8.7 - - + -
140Z ASN* 4.3 7.4 - - - +
141Z GLN* 4.4 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 142 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
200H LYS* 3.5 22.0 + - - -
6I MET* 3.5 28.7 - - + -
7I THR* 2.9 41.4 + - - -
122I LYS* 4.4 3.7 + - - -
123I ASP* 3.3 40.3 - - + -
124I PHE* 4.0 14.6 - + + -
138I CYS* 2.9 22.4 + - - +
139I GLU 4.3 1.4 + - - +
140I SER 3.4 1.0 - - - -
141I LEU* 1.3 79.0 - - - +
143I GLU* 1.3 86.7 + - - +
144I PRO* 3.8 16.2 - - + +
145I ASN 5.0 0.2 + - - -
146I LEU* 4.9 2.5 - - + -
151I LEU* 4.8 2.7 - - + -
154I THR* 4.6 3.8 - - - -
----------------------------------------------------------
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