Contacts of the strand formed by residues 103 - 112 (chain I) in PDB entry 2WQT
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 ARG 103 (chain I).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101I GLN 4.0 0.7 - - - -
102I PRO* 1.3 77.0 - - - +
104I ILE* 1.3 58.7 - - - +
139I VAL* 3.3 2.9 - - - -
140I VAL* 2.7 51.6 + - + +
147I TRP* 3.3 63.9 - - - +
236I MET* 3.8 33.2 - - + +
237I VAL 3.2 19.1 - - - +
238I ALA* 3.7 15.7 - - - +
239I VAL* 3.9 4.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 104 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103I ARG* 1.3 72.2 - - - +
105I GLU* 1.3 61.2 + - - +
137I LEU* 4.2 19.7 - - + -
138I GLU 3.2 9.2 - - - +
139I VAL* 3.5 32.5 - - + -
185I MET* 3.9 13.5 - - + +
236I MET* 3.2 4.8 - - - -
237I VAL* 3.0 46.1 + - + +
239I VAL* 3.4 14.8 - - + -
245I PHE* 3.1 49.4 - - + -
257I ALA* 6.0 0.7 - - + -
259I PHE* 4.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104I ILE* 1.3 75.8 - - - +
106I ALA* 1.3 60.2 + - - +
107I GLU* 3.1 18.8 - - - +
137I LEU* 3.4 8.1 - - - +
138I GLU* 2.8 43.2 + - + +
140I VAL* 3.7 8.6 - - - +
185I MET* 4.4 6.3 - - - -
232I ALA* 3.5 24.4 - - + +
234I GLY 4.2 5.8 - - - +
235I PRO 5.2 0.2 - - - -
236I MET* 3.7 24.6 + - + +
1262I PO4 2.8 47.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105I GLU* 1.3 74.1 - - - +
107I GLU* 1.3 63.9 + - - +
136I ALA 3.6 6.7 - - - +
137I LEU* 4.2 2.2 - - + -
183I MET* 3.7 38.0 - - + +
185I MET* 4.5 6.4 - - - +
232I ALA* 3.6 0.5 - - - -
233I LEU* 2.9 30.9 + - + +
234I GLY 5.1 1.0 + - - -
247I ALA* 3.8 22.7 - - + -
249I ILE* 4.6 3.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 107 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61I VAL 4.5 1.8 - - - +
105I GLU* 3.1 33.9 - - + +
106I ALA* 1.3 81.2 - - - +
108I ILE* 1.3 66.7 + - - +
135I PRO 3.8 0.2 - - - -
136I ALA* 2.9 40.5 + - + +
138I GLU* 3.1 23.4 - - + +
229I LEU* 3.3 23.0 - - + +
231I GLY* 3.0 37.0 + - - +
232I ALA* 3.5 8.2 + - - +
233I LEU* 4.0 6.7 - - - +
249I ILE* 3.6 7.4 - - - +
1262I PO4 4.0 1.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 108 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I GLU* 1.3 76.5 - - - +
109I ALA* 1.3 64.0 + - - +
110I LEU* 4.1 22.7 - - + -
133I VAL* 4.2 13.5 - - + -
134I LEU 3.9 4.5 - - - +
178I LEU* 4.2 9.0 - - + -
181I CYS* 3.5 32.1 - - - -
204I PRO* 3.9 22.2 - - + -
229I LEU* 4.0 0.6 - - - -
230I THR* 2.6 47.1 + - - +
231I GLY 4.4 1.6 + - - -
233I LEU* 4.1 18.0 - - + +
249I ILE* 4.4 5.2 - - + -
252I ILE* 3.7 18.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 109 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107I GLU 4.0 0.6 + - - -
108I ILE* 1.3 73.8 - - - +
110I LEU* 1.3 64.4 + - - +
133I VAL* 3.4 5.7 - - - +
134I LEU* 2.8 49.8 + - + +
136I ALA* 4.1 8.3 - - + -
166I ILE* 4.9 2.5 - - + -
227I ILE* 4.2 17.0 - - + -
228I ILE 3.3 6.3 - - - +
229I LEU* 3.7 22.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108I ILE* 4.1 11.7 - - + -
109I ALA* 1.3 83.7 - - - +
111I VAL* 1.3 65.4 + - - +
112I LEU* 5.1 4.3 - - + -
126I LEU* 4.7 0.4 - - + -
130I ILE* 4.4 20.4 - - + -
132I TRP 3.5 3.1 - - - +
133I VAL* 3.8 20.9 - - + -
178I LEU* 5.3 3.4 - - + -
204I PRO* 6.1 0.4 - - + -
205I LEU* 3.7 31.6 - - + -
208I ALA* 3.8 16.2 - - + -
226I ASP 3.7 0.5 - - - +
227I ILE* 3.3 6.4 - - - +
228I ILE* 2.8 45.7 + - + +
230I THR* 3.7 24.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124H ASP* 4.7 14.4 - - + +
128H ASN* 6.0 2.0 - - + -
110I LEU* 1.3 79.0 - - - +
112I LEU* 1.3 58.9 + - - +
130I ILE* 3.6 4.2 - - - +
131I GLU* 2.6 49.1 + - - +
132I TRP* 3.0 27.0 + - + +
134I LEU* 3.9 22.9 - - + -
225I GLY* 3.9 22.9 - - - +
226I ASP 3.4 2.7 - - - -
227I ILE* 4.4 15.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 112 (chain I).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I LEU* 5.1 7.6 - - + -
111I VAL* 1.3 78.7 - - - +
113I ASN* 1.4 58.8 + - - +
114I ARG 3.9 13.5 - - - +
116I LEU* 4.0 21.8 - - + -
126I LEU* 5.2 5.2 - - + -
129I ALA* 3.2 19.5 - - + +
130I ILE* 5.0 5.6 - - + -
131I GLU* 3.9 10.7 - - - +
222I LEU* 3.8 28.9 - - + -
223I ARG 3.9 14.8 - - - +
224I THR* 4.1 0.3 + - - -
225I GLY* 2.9 26.7 + - - -
226I ASP* 3.2 21.5 + - + +
228I ILE* 3.9 26.2 - - + -
----------------------------------------------------------
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