Contacts of the helix formed by residues 103 - 122 (chain B) in PDB entry 2CUY
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 GLU 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 5.8 0.9 - - - +
102B LEU* 1.3 77.7 - - - +
104B LEU* 1.3 67.2 + - - +
105B GLU* 4.4 12.4 - - - +
106B ASP* 3.2 25.3 + - - +
107B ALA* 2.9 22.8 + - - +
213B PRO* 5.1 9.2 - - - +
215B ARG* 5.6 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B VAL* 4.0 33.2 - - + +
33B ARG* 3.9 35.9 - - + +
34B ALA* 5.2 0.2 - - + -
64B LEU* 3.5 30.1 - - + -
65B ALA* 5.0 3.1 - - - -
68B TYR* 4.0 22.7 - - + -
97B VAL* 4.0 17.6 - - + +
102B LEU 3.9 1.0 + - - -
103B GLU* 1.3 72.3 - - - +
105B GLU* 1.3 67.2 + - - +
107B ALA* 3.2 3.7 + - - +
108B LEU* 2.8 45.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG* 2.9 56.7 + - - +
37B ALA* 4.3 15.6 - - + +
103B GLU* 3.3 9.6 - - + +
104B LEU* 1.3 78.0 + - - +
106B ASP* 1.3 64.2 + - - +
108B LEU* 3.4 8.0 + - - +
109B ARG* 3.2 50.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU* 4.7 2.0 - - + -
103B GLU* 3.2 33.3 + - - +
105B GLU* 1.3 78.2 - - - +
107B ALA* 1.3 58.0 + - - +
109B ARG* 3.3 22.4 + - - +
110B LEU* 2.9 35.3 + - - +
212B VAL* 3.7 38.4 - - + +
213B PRO* 4.2 11.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B LEU* 3.9 14.1 - - + -
93B TRP* 4.9 3.4 - - + -
97B VAL* 3.3 33.9 - - + -
102B LEU* 3.8 17.8 - - + +
103B GLU 2.9 10.9 + - - +
104B LEU 3.6 3.4 - - - +
106B ASP* 1.3 77.4 - - - +
108B LEU* 1.3 56.0 + - - +
110B LEU* 3.1 3.9 + - - +
111B VAL* 2.8 36.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B ARG 4.7 0.2 - - - +
34B ALA* 3.7 27.1 - - + +
37B ALA* 4.3 12.8 - - + -
38B LEU* 3.7 19.3 - - + +
41B LEU* 4.5 3.1 - - + -
61B PRO* 3.6 35.4 - - + +
64B LEU* 4.0 12.5 - - + +
65B ALA* 4.2 9.9 - - + -
104B LEU* 2.8 49.2 + - + +
105B GLU* 3.7 4.9 - - - +
107B ALA* 1.3 73.2 - - - +
109B ARG* 1.3 63.7 + - - +
111B VAL* 3.4 6.9 - - - +
112B ARG* 3.2 22.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B ALA* 4.2 19.1 + - + +
38B LEU* 4.6 17.0 - - + -
105B GLU* 3.2 38.9 + - - +
106B ASP* 3.5 28.7 + - - +
108B LEU* 1.3 79.1 - - + +
110B LEU* 1.3 63.8 + - + +
112B ARG* 3.3 6.7 + - - +
113B LEU* 3.2 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B TRP* 3.7 20.6 - - + -
102B LEU* 4.1 11.7 - - + -
106B ASP 2.9 20.9 + - - +
107B ALA 3.5 4.3 - - - +
109B ARG* 1.3 78.9 - - + +
111B VAL* 1.3 58.2 + - - +
113B LEU* 3.4 8.2 + - + +
114B ARG* 2.8 27.0 + - - +
205B LEU* 3.7 13.1 - - + +
208B ASP* 3.8 39.7 - - + +
209B LEU* 3.6 29.8 - - + +
212B VAL* 3.7 20.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60B GLN* 3.2 17.5 - - + +
61B PRO* 3.7 26.5 - - + -
64B LEU* 3.9 12.6 - - + -
90B LEU* 3.6 28.0 - - + -
93B TRP* 3.8 30.7 - - + -
107B ALA 2.8 25.4 + - - +
108B LEU* 3.4 13.2 - - - +
110B LEU* 1.3 70.2 - - - +
112B ARG* 1.3 59.5 + - - +
113B LEU 3.3 0.2 - - - -
114B ARG* 3.6 7.2 - - - -
115B GLY* 2.9 22.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B LEU* 3.6 42.4 + - + +
39B PRO 4.9 4.8 + - - -
41B LEU* 4.3 20.8 - - - +
44B LEU* 5.6 2.8 - - - +
57B GLU* 3.0 33.2 + - + +
58B ASN* 3.0 28.8 + - - +
61B PRO* 3.8 8.4 - - + +
108B LEU 3.2 13.2 + - - +
109B ARG* 3.6 10.3 - - - +
111B VAL* 1.3 74.1 - - - +
113B LEU* 1.3 64.6 + - + +
115B GLY 3.2 1.0 + - - -
116B ARG* 2.9 52.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ARG* 3.2 19.1 + - + +
110B LEU* 3.6 9.6 - - + +
112B ARG* 1.3 78.4 - - + +
114B ARG* 1.3 56.7 + - - +
116B ARG* 3.1 27.3 + - - +
117B TYR* 2.6 69.9 + - + +
205B LEU* 4.5 2.2 - - + -
208B ASP* 3.5 35.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 4.6 0.6 + - - -
60B GLN* 2.7 44.9 + - - +
89B SER* 2.9 24.2 + - - -
90B LEU* 4.1 12.7 - - - +
93B TRP* 3.3 37.4 - - - +
110B LEU 2.8 18.3 + - - +
111B VAL* 3.5 9.6 - - - +
112B ARG 3.3 0.2 - - - -
113B LEU* 1.3 76.6 - - - +
115B GLY* 1.3 56.8 + - - +
117B TYR* 3.4 5.5 + - - +
118B MET* 3.0 62.5 + - + +
194B HIS* 4.4 2.2 - - - -
205B LEU* 4.2 19.9 - - + +
243B GLN* 2.9 25.7 + - - -
244B ILE* 4.3 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56B THR* 2.7 50.9 + - - -
57B GLU 3.8 2.9 - - - -
60B GLN* 3.5 7.8 + - - -
111B VAL 2.9 13.1 + - - -
112B ARG 3.7 2.5 - - - -
114B ARG* 1.3 77.0 - - - +
116B ARG* 1.3 55.1 + - - +
118B MET* 3.4 2.0 + - - +
119B GLN* 3.0 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57B GLU* 3.5 39.4 + - + +
112B ARG* 2.9 39.0 + - - +
113B LEU* 3.6 27.9 - - - +
115B GLY* 1.3 72.0 - - - +
117B TYR* 1.3 72.9 + - + +
119B GLN* 3.1 9.2 + - + +
120B GLU* 3.0 47.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B LEU* 2.6 51.4 + - + +
114B ARG* 3.6 5.2 - - - +
116B ARG* 1.3 81.4 - - + +
118B MET* 1.3 61.7 + - - +
120B GLU* 3.3 4.6 + - - +
121B ALA* 3.0 22.7 + - - +
201B ALA* 3.7 22.0 - - + +
204B ARG* 3.4 50.3 + - + +
205B LEU* 3.6 35.4 - - + -
208B ASP* 2.7 31.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLN* 4.1 1.8 - - - +
56B THR* 4.8 0.7 - - - +
60B GLN* 3.5 25.6 - - - -
89B SER* 5.2 1.3 - - - +
114B ARG* 3.0 53.5 + - + +
115B GLY* 3.6 4.7 - - - +
117B TYR* 1.3 76.5 - - - +
119B GLN* 1.3 63.9 + - - +
121B ALA* 3.3 15.4 + - - +
122B VAL 4.6 0.3 + - - -
191B ALA* 3.7 11.7 - - - +
193B PHE* 4.0 25.4 - - + -
194B HIS* 5.4 5.6 - - - +
198B MET* 3.5 27.9 - - + +
201B ALA* 3.9 8.1 - - + -
244B ILE* 3.8 30.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B LEU* 5.1 14.4 - - + +
56B THR* 3.6 13.2 + - - +
57B GLU* 5.1 7.9 - - + +
115B GLY 3.0 13.8 + - - +
116B ARG* 3.1 15.2 + - + +
118B MET* 1.3 78.6 - - - +
120B GLU* 1.3 66.8 + - + +
121B ALA 3.8 0.2 + - - -
122B VAL 4.2 8.7 - - - +
124B VAL* 4.2 23.2 - - - +
191B ALA* 5.0 9.6 - - - +
193B PHE* 6.2 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 3.0 36.2 + - - +
117B TYR 3.7 1.6 - - - +
119B GLN* 1.3 83.1 - - + +
121B ALA* 1.3 67.0 + - - +
122B VAL* 3.5 6.5 + - - +
123B PRO* 5.7 0.2 - - - +
204B ARG* 2.7 45.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR 3.0 12.1 + - - +
118B MET* 3.3 15.7 + - - +
120B GLU* 1.3 80.6 - - - +
122B VAL* 1.3 61.9 + - - +
123B PRO* 4.3 3.1 - - - +
191B ALA* 5.9 0.2 - - + -
197B LEU 4.3 4.7 - - - +
198B MET* 4.0 23.1 - - + -
200B PRO* 3.9 32.0 - - + +
201B ALA* 4.4 6.1 - - + +
204B ARG* 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B MET 4.6 1.2 + - - -
119B GLN 4.2 12.5 - - - +
120B GLU* 4.3 4.4 - - - -
121B ALA* 1.3 81.0 - - + +
123B PRO* 1.3 87.1 - - + +
124B VAL* 3.4 2.8 + - - +
126B GLU* 3.8 20.0 - - + +
127B GLY* 4.1 11.7 - - - +
191B ALA* 5.5 3.4 - - - +
192B PRO* 3.6 31.2 - - + +
197B LEU* 3.5 36.3 - - + +
----------------------------------------------------------
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