Contacts of the strand formed by residues 93 - 103 (chain D) in PDB entry 1S7X
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 HIS 93 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D ALA 3.7 0.9 - - - +
12D VAL* 3.3 6.5 - - - +
13D SER* 3.0 45.9 + - - +
78D LEU* 4.9 7.2 - - + +
82D LEU* 3.3 23.3 - - + +
87D GLN* 3.5 29.4 - - + -
88D SER 4.4 7.2 + - - -
91D GLY* 3.9 23.1 + - - -
92D SER* 1.3 81.8 + - - +
94D THR* 1.3 65.2 + - - +
118D TYR* 3.3 19.2 + - + +
119D GLU* 2.6 26.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 4.4 6.1 - - + -
11D ALA 3.5 7.0 - - - +
12D VAL* 4.4 7.8 - - + +
78D LEU* 4.4 0.9 - - - -
92D SER 5.5 0.2 - - - -
93D HIS* 1.3 77.8 + - - +
95D LEU* 1.3 63.1 + - - +
96D GLN* 3.9 30.1 - - + +
118D TYR* 3.0 11.5 - - - -
119D GLU* 2.9 33.5 + - - -
120D GLY 5.3 0.2 - - - -
31E HIS* 3.6 28.0 + - + -
32E PRO* 4.8 2.6 - - - +
33E PRO* 4.0 11.7 - - + +
62E PHE* 4.3 12.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D THR* 3.4 3.1 - - - +
11D ALA 2.9 32.5 + - - +
73D TRP* 4.5 2.7 - - + -
74D PHE* 3.7 32.7 - - + +
77D SER* 3.6 30.5 - - - -
78D LEU* 3.2 27.6 - - + -
81D LEU* 4.0 13.5 - - + -
94D THR* 1.3 74.2 - - - +
96D GLN* 1.3 65.0 + - - +
116D PHE* 4.9 0.7 - - + -
117D ALA 3.3 18.4 - - - +
118D TYR* 4.6 3.4 - - + -
123D TYR* 5.8 0.4 - - + -
9F MET* 4.0 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU 3.2 7.9 - - - +
10D THR* 4.0 12.1 - - + +
74D PHE* 4.5 2.5 - - - -
94D THR* 3.9 14.5 - - + +
95D LEU* 1.3 79.2 - - - +
97D GLN* 1.3 62.0 + - - +
116D PHE* 3.2 8.0 - - - +
117D ALA* 2.9 34.6 + - - +
120D GLY* 3.6 25.5 + - - -
56E PHE* 3.3 30.7 - - + -
60E TRP* 2.9 49.8 + - + +
62E PHE* 3.7 12.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7D TYR 3.6 1.3 - - - +
8D PHE* 3.5 4.5 - - - -
9D GLU* 2.9 52.1 + - + +
74D PHE* 3.2 27.2 - - + -
96D GLN* 1.3 76.4 - - - +
98D MET* 1.3 70.8 + - - +
99D SER* 4.1 1.9 + - - +
114D LEU* 3.6 16.7 - - + +
115D GLN 3.3 9.4 - - - +
116D PHE* 3.3 23.5 - - + -
56E PHE* 3.8 1.4 - - - -
60E TRP* 4.2 1.3 - - - -
3F VAL* 3.7 8.1 - - - +
5F ASN* 2.9 39.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ARG* 5.2 5.4 - - - +
7D TYR 3.6 3.8 - - - -
8D PHE* 3.4 43.5 - - + -
97D GLN* 1.3 73.9 - - - +
99D SER* 1.3 60.7 + - - +
113D TYR* 4.1 2.4 - - + -
114D LEU* 3.3 4.7 + - - +
115D GLN* 2.8 60.3 + - + +
56E PHE* 3.7 16.2 - - + -
58E LYS* 3.4 38.8 - - + +
60E TRP* 3.4 32.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D ARG* 3.3 11.8 - - - -
7D TYR* 3.0 41.3 + - - +
9D GLU* 4.4 1.2 + - - -
97D GLN* 4.1 3.9 + - - -
98D MET* 1.3 77.4 - - - +
100D GLY* 1.3 58.7 + - - +
113D TYR* 3.0 12.6 - - - -
114D LEU* 4.2 14.4 - - - -
159D TYR* 5.0 5.7 + - - -
160D LEU* 5.1 1.1 - - - -
3F VAL* 3.4 33.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 100 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D MET 3.3 11.7 - - - -
6D ARG* 4.0 6.1 - - - -
7D TYR* 6.1 0.4 - - - -
99D SER* 1.3 76.8 - - - +
101D CYS* 1.3 61.9 + - - -
112D GLY* 3.6 0.3 - - - -
113D TYR* 2.8 32.8 + - - +
159D TYR* 4.7 5.4 - - - -
160D LEU* 3.2 11.7 - - - +
164D CYS* 3.7 13.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 101 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D SER* 3.2 4.2 - - - -
5D MET* 3.0 31.3 + - - -
6D ARG* 3.3 3.6 + - - +
100D GLY* 1.3 73.3 - - - +
102D ASP* 1.3 66.1 + - - +
103D LEU* 4.1 1.7 + - + -
109D LEU* 3.8 22.4 - - + -
111D ARG 3.5 4.7 - - - +
112D GLY* 4.8 1.3 - - - -
113D TYR* 4.5 0.2 - - - -
160D LEU* 4.1 5.2 - - + +
164D CYS* 2.1 57.9 - - - -
165D VAL* 3.9 7.0 - - + -
168D LEU* 4.3 12.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 102 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3D HIS 3.6 4.9 - - - +
4D SER* 3.6 9.5 - - - -
6D ARG* 3.0 29.8 + - - -
101D CYS* 1.3 72.4 - - - +
103D LEU* 1.3 57.2 + - - +
109D LEU* 3.7 5.5 - - - +
110D LEU* 2.8 45.0 + - + -
111D ARG* 2.9 15.7 + - + +
113D TYR* 2.9 28.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 103 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2D PRO* 3.5 6.4 - - - +
3D HIS* 2.9 37.2 + - + +
101D CYS* 5.1 2.2 - - - -
102D ASP* 1.3 78.1 - - - +
104D GLY* 1.3 66.4 + - - +
107D TRP* 3.6 22.2 - - + +
108D ARG 3.3 13.7 - - - +
109D LEU* 3.9 7.6 - - + +
110D LEU* 4.3 5.5 - - - +
165D VAL* 4.1 20.4 - - + -
168D LEU* 3.5 33.9 - - + -
169D HIS* 3.7 27.4 - - + -
172D LEU* 4.3 11.2 - - + -
----------------------------------------------------------
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