Contacts of the strand formed by residues 103 - 112 (chain D) in PDB entry 2Q6W
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 ASN 103 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 3.3 14.7 - - - -
94D ASN* 3.5 4.4 + - - +
95D SER* 3.1 25.7 + - - -
96D PRO 3.0 27.5 + - - -
97D VAL* 3.5 12.1 - - - +
98D GLU 4.7 1.0 - - - +
101D GLU* 4.0 6.0 + - - +
102D PRO* 1.3 77.1 + - - +
104D VAL* 1.3 89.5 + - - +
152D PRO* 3.0 6.8 - - - +
153D PHE* 2.8 48.9 + - + +
155D PRO* 4.4 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 104 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93D THR* 3.0 6.9 - - - -
94D ASN* 2.8 41.3 + - + +
103D ASN* 1.3 92.6 + - - +
105D LEU* 1.3 73.1 + - - +
106D ILE* 4.5 2.5 - - + -
150D TYR* 3.7 31.4 - - + -
151D LEU 3.3 8.7 - - - +
152D PRO* 4.2 11.4 - - + -
153D PHE* 3.8 3.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 105 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91D VAL* 4.3 2.5 - - + -
92D LEU 3.7 6.7 - - - +
93D THR* 3.2 30.3 - - + -
104D VAL* 1.3 74.6 - - - +
106D ILE* 1.3 60.8 + - - +
121D TRP* 3.4 22.0 - - + -
150D TYR* 3.1 6.2 - - - -
151D LEU* 2.5 40.0 + - + +
153D PHE* 3.4 17.0 - - + -
161D TYR* 3.4 46.0 - - + -
178D TRP* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 106 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90D THR 3.6 0.7 - - - +
91D VAL* 3.1 4.2 - - - +
92D LEU* 2.5 45.1 + - + +
93D THR 4.4 1.1 - - - -
94D ASN* 4.1 23.3 - - + +
104D VAL* 4.4 3.8 - - + +
105D LEU* 1.3 75.4 - - - +
107D CYS* 1.3 61.7 + - - +
108D PHE* 3.3 36.1 - - + -
121D TRP* 3.9 2.7 - - - -
148D PHE* 3.8 13.9 - - + -
149D HIS 3.5 5.2 - - - +
150D TYR* 3.7 33.4 - - + -
150E ASN* 4.1 10.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 107 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89D VAL* 3.6 23.8 - - - -
90D THR 3.3 3.1 - - - -
91D VAL* 4.1 2.2 - - - +
106D ILE* 1.3 76.4 - - - +
108D PHE* 1.3 60.9 + - - +
109D ILE* 3.7 14.2 + - - +
121D TRP* 3.5 16.7 - - + -
147D LYS 3.9 0.2 - - - +
148D PHE* 3.4 5.2 - - - -
149D HIS* 2.9 30.2 + - + +
163D CYS* 2.1 49.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 108 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88D GLU 3.2 2.3 - - - +
89D VAL* 3.1 7.1 - - - +
90D THR* 2.8 53.2 + - + +
92D LEU* 1.9 44.6 - - + -
106D ILE* 3.3 21.3 - - + -
107D CYS* 1.3 69.2 - - - +
109D ILE* 1.3 62.5 + - - +
110D ASP* 3.9 7.4 - - + -
146D ARG* 6.1 0.4 - - - -
147D LYS 4.0 4.3 - - - -
148D PHE* 3.4 21.8 - + + -
148E ILE* 3.4 22.9 - - + -
149E GLN 3.1 25.6 - - - -
150E ASN* 4.0 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 109 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PRO* 3.3 29.4 - - + -
88D GLU 3.4 2.5 - - - -
89D VAL* 4.2 1.8 - - + -
107D CYS* 3.9 19.1 - - - +
108D PHE* 1.3 77.2 - - - +
110D ASP* 1.3 58.8 + - - +
112D PHE* 3.2 19.1 - - + -
117D VAL* 4.3 4.5 - - + -
119D VAL* 3.3 37.9 - - + -
146D ARG* 3.1 4.4 - - - +
147D LYS* 2.9 38.5 + - + +
149D HIS* 3.7 17.9 - - + +
165D VAL* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D PRO* 3.3 3.1 - - - +
88D GLU* 2.8 41.3 + - + +
108D PHE* 4.8 7.2 - - + -
109D ILE* 1.3 78.1 - - - +
111D LYS* 1.3 91.5 + - + +
112D PHE* 3.3 3.1 - - - -
140D ARG* 3.1 27.7 + - - -
145D PHE 3.6 1.6 - - - -
146D ARG* 3.2 26.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 111 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A GLU* 3.1 24.7 - - - +
111A LYS* 4.8 9.6 - - + +
85D VAL* 3.2 21.3 - - - +
86D PRO 3.4 6.8 - - - +
88D GLU* 3.3 26.5 - - + +
110D ASP* 1.3 94.9 + - - +
112D PHE* 1.3 57.6 + - - +
140D ARG* 3.2 40.4 - - - +
142D ASP* 4.7 2.5 - - - +
144D LEU* 3.7 16.1 - - + +
145D PHE 2.8 10.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 112 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85D VAL* 3.2 16.6 - - - +
87D PRO* 3.5 19.5 - - + -
109D ILE* 3.2 40.8 - - + -
110D ASP 3.8 4.7 - - - -
111D LYS* 1.3 78.5 - - - +
113D THR* 1.3 62.2 + - - +
114D PRO 3.5 20.2 - - - -
115D PRO* 3.9 2.7 - - + -
117D VAL* 3.8 14.1 - - + -
137D PHE* 3.5 40.6 - + - -
144D LEU* 3.5 3.3 - - - -
145D PHE* 2.8 47.1 + - + -
146D ARG* 3.7 5.2 - - - -
147D LYS* 4.0 7.0 - - + -
167D HIS* 3.6 9.4 - + - -
----------------------------------------------------------
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