Contacts of the strand formed by residues 91 - 99 (chain D) in PDB entry 6H7L
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 91 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ARG* 4.0 16.4 - - + -
39D GLN 3.5 11.9 - - - +
40D ALA* 3.5 26.7 - - + +
41D PRO* 5.0 3.1 - - - -
89D ASP 3.1 9.8 + - - +
90D THR* 1.3 77.6 - - - +
92D VAL* 1.3 60.7 + - - +
93D TYR* 3.4 9.1 - - + -
115D GLN* 3.9 9.0 - - - +
116D VAL 3.1 28.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 92 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38D ARG* 3.3 2.6 - - - -
39D GLN* 3.0 34.1 + - + +
91D ALA* 1.3 72.8 - - - +
93D TYR* 1.3 59.6 + - - +
94D TYR* 3.5 42.5 - - + +
112D GLN 5.0 0.7 - - - +
113D GLY* 4.2 2.9 - - - -
114D THR 3.7 20.9 - - - +
115D GLN* 3.5 21.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 93 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU* 3.9 2.1 - - - +
20D LEU* 3.8 28.7 - - + -
36D TRP* 4.2 7.9 - + + -
37D TYR 3.3 8.1 - - - +
38D ARG* 3.0 37.5 + - + -
48D VAL* 3.9 17.7 - - + -
67D PHE* 3.8 5.9 - - - -
80D LEU* 4.4 3.8 - - + -
82D MET* 3.9 19.0 - - - -
89D ASP* 3.0 35.1 + - - +
91D ALA* 3.4 16.2 - - + -
92D VAL* 1.3 73.9 - - - +
94D TYR* 1.3 61.3 + - - +
113D GLY* 3.3 1.4 - - - -
114D THR* 2.9 39.6 + - + +
116D VAL* 3.5 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 94 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D GLU* 3.5 2.7 - - - -
36D TRP* 3.4 8.4 - - - -
37D TYR* 2.7 43.4 + - - +
38D ARG* 4.7 3.4 - - - -
39D GLN* 4.1 26.2 + - + +
45D ARG* 4.2 26.9 - - - -
92D VAL* 3.5 39.6 - - + +
93D TYR* 1.3 72.8 - - - +
95D CYS* 1.3 62.1 + - - +
96D ASN 3.9 0.2 + - - -
110D TRP* 3.9 21.3 - + + -
111D GLY 3.4 20.2 - - - +
112D GLN 3.3 18.8 - - - -
113D GLY* 3.7 8.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 95 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.5 14.2 - - + +
6D GLU* 2.8 22.4 + - + +
22D CYS* 2.0 54.5 - - + -
34D MET* 5.1 0.2 - - - -
35D GLY 3.4 9.6 - - - -
36D TRP* 4.0 6.2 - - + -
78D VAL* 4.4 7.9 - - - -
94D TYR* 1.3 72.2 - - - +
96D ASN* 1.3 65.5 - - - +
97D VAL* 4.7 4.0 - - - -
110D TRP* 3.5 4.4 - - - -
111D GLY 2.9 25.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33D ILE* 3.7 1.6 - - - +
34D MET* 3.4 4.2 - - - +
35D GLY* 2.8 34.7 + - - +
37D TYR* 3.4 33.3 + - + -
94D TYR 3.9 0.4 + - - -
95D CYS* 1.3 73.7 - - - +
97D VAL* 1.3 75.9 + - - +
98D LYS* 3.0 30.7 + - - +
108D ASP* 3.8 6.1 + - - -
109D TYR 2.8 25.3 + - - +
110D TRP* 3.4 30.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 97 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4D LEU* 3.7 29.2 - - + -
24D ALA* 4.5 2.5 - - + -
28D ILE* 4.1 29.6 - - + -
32D ASN* 4.8 1.6 - - + -
33D ILE 3.3 7.0 - - - +
34D MET* 4.0 27.8 - - + -
95D CYS* 4.7 2.2 - - - -
96D ASN* 1.3 82.7 + - - +
98D LYS* 1.3 67.8 - - - +
99D ASP 4.4 0.7 - - - +
107D TYR 3.6 1.7 - - - +
108D ASP* 3.5 4.0 - - - -
109D TYR* 2.9 49.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 98 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B GLN* 6.1 2.2 - - - +
32D ASN* 3.2 9.7 - - - +
33D ILE* 2.8 59.5 + - + +
37D TYR* 3.7 17.5 + - - -
96D ASN* 3.0 24.0 + - - +
97D VAL* 1.3 71.2 - - - +
99D ASP* 1.3 60.3 + - - +
100D PHE* 3.9 12.8 + - + -
106D ASP* 4.0 17.7 - - + +
107D TYR 3.7 4.5 - - - -
108D ASP* 3.1 28.8 + - - +
110D TRP* 5.0 2.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284B LYS* 2.7 36.7 + - - +
287B LYS* 5.3 0.2 + - - -
28D ILE* 3.7 8.1 - - + +
29D PHE* 3.2 26.4 + - - +
32D ASN* 4.4 5.6 - - - -
97D VAL* 3.9 1.2 + - + -
98D LYS* 1.3 71.8 - - - +
100D PHE* 1.3 59.3 + - - +
101D GLY* 2.7 33.8 + - - -
102D ALA 5.0 0.2 + - - -
105D TYR 4.3 0.5 - - - +
106D ASP* 3.4 5.2 - - - -
107D TYR* 2.9 41.4 + - + +
109D TYR* 4.0 15.2 - - + -
----------------------------------------------------------
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