Contacts of the strand formed by residues 186 - 200 (chain A) in PDB entry 1SCR
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 186 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LEU* 3.9 29.4 - - + -
116A LYS 3.5 12.1 - - - +
117A SER* 3.8 4.5 - - - +
182A TRP* 5.6 2.0 - - + -
183A GLU* 3.1 22.8 + - + +
184A SER 3.4 2.5 - - - +
185A SER* 1.3 77.4 + - - +
187A VAL* 1.3 61.5 + - - +
188A VAL 4.5 6.5 - - - +
189A ALA* 5.2 1.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 187 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56A SER* 4.4 2.9 + - - -
57A VAL* 4.1 10.0 - - - +
116A LYS* 2.8 23.9 + - + +
117A SER 4.2 6.3 - - - +
118A ASN* 3.7 31.6 - - + +
185A SER 4.1 1.6 - - - +
186A ALA* 1.3 75.2 - - - +
188A VAL* 1.3 70.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 188 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A ASN* 4.7 10.3 - - + -
56A SER* 3.6 4.9 - - - +
57A VAL* 3.9 22.0 - - + -
114A LYS 4.0 0.7 - - - +
115A LEU* 3.6 0.5 - - - -
116A LYS* 2.9 65.9 + - + +
186A ALA* 3.6 3.4 - - - +
187A VAL* 1.3 87.5 - - + +
189A ALA* 1.3 72.3 + - - +
190A SER* 4.9 4.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 189 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 4.9 3.2 - - + -
55A ASN* 3.2 2.9 - - - +
56A SER* 2.8 43.9 + - - +
82A ASP* 5.9 0.7 - - - +
114A LYS 3.2 7.4 - - - +
115A LEU* 3.5 25.1 - - + -
181A ILE* 3.6 16.4 - - - +
182A TRP* 5.3 0.9 - - - -
186A ALA* 5.3 2.0 - - + -
188A VAL* 1.3 74.1 - - - +
190A SER* 1.3 62.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 190 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A TYR* 3.4 15.7 - - - -
55A ASN* 3.7 11.4 - - - +
113A SER* 3.4 4.7 + - - -
114A LYS* 2.9 51.6 + - - +
116A LYS* 5.2 4.7 + - - -
188A VAL* 4.9 6.1 - - - +
189A ALA* 1.3 76.2 - - - +
191A PHE* 1.3 64.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 191 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE* 4.1 23.3 - - + -
53A ILE* 3.5 2.6 - - - +
54A TYR* 3.1 67.4 + + + +
61A LEU* 4.0 11.7 - - + -
81A LEU* 3.9 8.7 - - + -
111A PHE* 3.8 28.0 - + + -
112A THR 3.1 14.1 - - - +
113A SER* 4.2 4.3 - - - +
181A ILE* 5.2 14.1 - - + -
190A SER* 1.3 75.3 - - - +
192A GLU* 1.3 70.9 + - - +
193A ALA 4.7 0.7 - - - -
212A PHE* 4.3 8.1 - + - -
214A ILE* 3.5 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 192 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52A ILE 3.3 7.9 - - - +
53A ILE* 4.2 16.4 - - + +
111A PHE* 3.4 4.9 - - - -
112A THR* 2.9 46.2 + - - +
114A LYS* 5.7 2.6 + - - -
191A PHE* 1.3 79.2 - - - +
193A ALA* 1.3 64.0 + - - +
194A THR* 5.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 193 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A ALA 4.0 0.2 - - - +
51A HIS* 3.4 1.9 - - - +
52A ILE* 2.8 42.9 + - + +
109A TRP* 4.9 2.2 - - - +
110A SER 3.3 9.0 - - - +
111A PHE* 3.9 17.7 - - + -
191A PHE* 4.7 1.3 - - + -
192A GLU* 1.3 76.7 - - - +
194A THR* 1.3 66.5 + - - +
195A PHE* 5.7 0.4 - - + -
212A PHE* 3.9 30.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 194 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49A THR* 4.0 10.5 - - + -
50A ALA 3.2 7.6 - - - +
51A HIS* 3.0 36.7 + - + +
108A SER* 6.1 0.4 - - - +
109A TRP* 3.4 3.5 - - - -
110A SER* 2.9 46.7 + - - +
192A GLU* 5.0 9.7 + - - +
193A ALA* 1.3 76.8 + - - +
195A PHE* 1.3 68.2 + - - +
196A THR* 5.2 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 195 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 6.5 0.2 - - + -
9A LEU* 4.1 16.8 - - + -
49A THR* 3.5 2.8 - - - +
50A ALA* 2.9 53.7 + - + -
52A ILE* 3.8 20.6 - - + -
93A LEU* 3.9 20.0 - - + -
106A ILE* 4.2 15.7 - - + -
108A SER* 3.3 15.3 - - - +
109A TRP* 4.1 14.1 - + + +
193A ALA 5.6 0.2 - - - -
194A THR* 1.3 79.4 - - - +
196A THR* 1.3 64.4 + - - +
197A PHE* 3.7 25.5 - + + -
210A ILE* 4.1 21.8 - - + -
212A PHE* 3.8 19.3 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 196 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A VAL* 4.3 11.2 - - + -
48A GLY 3.1 10.3 - - - -
49A THR* 3.3 26.7 - - + +
106A ILE* 3.5 6.9 - - - +
107A LEU* 3.0 35.0 + - - +
108A SER* 2.9 35.3 + - - +
194A THR* 5.2 3.8 - - + -
195A PHE* 1.3 78.6 - - - +
197A PHE* 1.3 60.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 197 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 3.6 24.0 - - + -
40A TRP* 4.0 12.1 - + - -
46A LYS 3.8 0.2 - - - +
47A VAL* 3.3 5.2 - - - +
48A GLY* 2.9 58.0 + - - -
49A THR 3.6 12.8 - - - -
50A ALA* 4.0 2.0 - - + -
65A VAL* 3.8 15.3 - - + -
67A TYR* 3.7 20.6 - + - -
105A THR 3.2 13.0 - - - +
106A ILE* 4.0 7.0 - - + -
107A LEU* 3.9 5.4 - - - -
195A PHE* 3.7 21.1 - + - -
196A THR* 1.3 76.5 - - - +
198A LEU* 1.3 61.5 + - - +
199A ILE* 4.2 22.7 - - + -
210A ILE* 3.9 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 198 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A GLY* 3.4 40.4 - - - +
46A LYS 3.9 4.3 - - - +
47A VAL* 3.8 22.0 - - + -
103A THR* 3.4 9.5 + - - -
105A THR* 2.9 38.0 + - + +
107A LEU* 3.8 17.5 - - + -
197A PHE* 1.3 74.0 - - - +
199A ILE* 1.3 66.6 + - - +
200A LYS* 4.3 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 199 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A LEU* 5.3 0.9 - - + -
11A THR* 3.8 26.0 - - + -
40A TRP* 4.0 18.6 - - + -
42A MET* 4.5 14.6 - - + -
43A GLN 4.1 2.5 + - - +
44A ASN* 3.8 5.1 - - - -
45A GLY* 2.8 23.4 + - - -
46A LYS 4.3 3.8 + - - -
67A TYR* 5.5 2.9 + - - +
102A GLU* 3.5 34.3 - - + +
103A THR 3.4 8.3 - - - +
104A ASN* 4.1 2.5 - - - +
197A PHE* 4.2 13.0 - - + -
198A LEU* 1.3 72.5 - - - +
200A LYS* 1.3 62.5 + - - +
206A PRO* 4.9 3.8 - - + -
210A ILE* 3.9 34.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 200 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A ASN* 3.4 10.3 - - - +
45A GLY* 3.8 14.1 - - - -
102A GLU* 3.4 2.4 - - - -
103A THR* 2.9 52.6 + - + +
105A THR* 5.7 0.8 + - - -
163A GLY 5.5 2.6 + - - -
165A PRO* 4.1 2.6 - - - +
198A LEU* 4.3 25.7 - - + +
199A ILE* 1.3 77.0 - - - +
201A SER* 1.3 64.6 + - - +
202A PRO* 4.7 0.2 - - - -
----------------------------------------------------------
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