Contacts of the helix formed by residues 92 - 107 (chain B) in PDB entry 1EKP
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 92 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B PHE* 1.3 79.5 - - + +
93B PRO* 1.3 69.1 - - - +
94B TRP* 3.1 15.7 + - + -
95B LEU* 3.2 42.8 + - + +
96B ASN* 3.3 9.4 + - - -
269B VAL* 4.3 9.9 - - + -
272B GLN* 4.2 4.0 - - - +
273B SER* 3.1 37.0 + - - +
276B ASP* 3.2 27.7 + - - -
361B TRP* 2.9 70.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 93 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B MET* 3.5 24.5 - - + -
90B LEU* 3.2 38.6 - - + +
91B PHE 3.1 1.3 - - - -
92B ARG* 1.3 90.4 - - - +
94B TRP* 1.3 71.7 + - + +
96B ASN* 3.0 18.7 + - - +
97B MET* 3.1 16.7 + - - +
118B LEU* 3.7 22.2 - - + -
363B PHE* 3.6 18.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 94 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.1 19.2 + - + -
93B PRO* 1.3 81.7 - - + +
95B LEU* 1.3 66.8 + - + +
97B MET* 3.3 9.1 + - - +
98B ASP* 3.1 27.8 + - - +
114B LYS* 5.3 0.2 - - - +
115B LEU* 4.4 16.9 - - + +
118B LEU* 3.8 22.5 - - + +
360B GLU 3.6 21.5 - - - -
361B TRP* 3.5 26.0 - + - -
362B MET 4.4 2.9 - - - -
363B PHE* 3.7 31.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 95 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ARG* 3.2 52.7 + - + +
94B TRP* 1.3 80.8 - - + +
96B ASN* 1.3 57.7 + - - +
98B ASP* 3.4 8.5 + - + +
99B ARG* 3.1 27.4 + - - +
102B ARG* 5.5 0.5 + - - -
269B VAL* 3.9 34.7 - - + +
272B GLN* 4.7 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 96 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 3.2 26.1 - - + +
77B GLY 3.2 22.7 - - - +
78B MET* 3.8 28.0 - - - +
91B PHE 4.1 4.0 + - - -
92B ARG 3.3 19.8 + - - -
93B PRO* 3.0 13.1 + - - +
95B LEU* 1.3 75.0 - - - +
97B MET* 1.3 64.7 + - + +
99B ARG* 3.3 8.7 + - - -
100B MET* 2.9 30.0 + - - +
269B VAL* 4.0 16.8 - - - +
370B PLP 4.8 0.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 97 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 5.7 1.1 - - + -
78B MET* 4.3 17.7 - - + -
93B PRO 3.1 18.6 + - - +
94B TRP* 3.3 10.3 + - + +
96B ASN* 1.3 81.0 - - + +
98B ASP* 1.3 61.8 + - - +
100B MET* 3.6 11.5 + - - +
101B LEU* 3.1 23.0 + - - +
112B PHE* 4.6 3.2 - - + -
114B LYS* 3.7 40.6 - - + +
117B LEU* 3.6 33.9 - - + -
118B LEU* 4.1 18.6 - - + -
121B ILE* 3.9 20.0 - - + -
144B PRO* 5.0 4.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 98 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B TRP* 3.1 15.2 + - - +
95B LEU* 3.6 13.5 - - + +
96B ASN 3.2 0.2 - - - -
97B MET* 1.3 76.2 - - - +
99B ARG* 1.3 65.9 + - - +
101B LEU* 3.2 5.5 + - - +
102B ARG* 3.1 38.0 + - - +
114B LYS* 2.5 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 99 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76B GLU* 2.7 39.7 + - - +
77B GLY 4.3 3.6 + - - -
95B LEU 3.1 13.8 + - - +
96B ASN* 3.7 8.9 + - - +
98B ASP* 1.3 78.3 - - - +
100B MET* 1.3 63.4 + - - +
102B ARG* 3.3 30.1 + - - +
103B SER* 3.0 30.9 + - - +
200B ASN 5.6 1.6 - - - +
201B TYR* 5.4 1.7 - - + -
202B LYS* 3.8 20.7 - - + +
266B LEU* 3.3 27.1 - - + +
267B PRO* 2.8 42.3 + - + -
268B GLY* 3.6 1.2 - - - -
269B VAL* 3.7 11.5 - - - +
370B PLP 2.9 29.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 100 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.9 16.5 - - + +
75B PHE 5.8 0.2 - - - -
76B GLU* 3.7 18.1 + - + -
96B ASN 2.9 18.1 + - - +
97B MET* 3.8 9.4 - - - +
99B ARG* 1.3 74.9 - - - +
101B LEU* 1.3 65.3 + - - +
103B SER* 3.3 7.0 + - - -
104B ALA* 2.9 23.1 + - + +
112B PHE* 4.2 10.3 - - + -
117B LEU* 4.0 22.4 - - + -
144B PRO* 4.0 29.6 - - + +
145B VAL 4.2 9.6 - - - +
146B LEU* 4.0 26.7 - - + -
163B LEU* 4.6 15.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B MET 3.1 18.4 + - - +
98B ASP* 3.2 6.0 + - - +
100B MET* 1.3 75.6 - - - +
102B ARG* 1.3 63.8 + - + +
104B ALA* 3.2 4.6 + - + +
105B MET* 3.1 41.6 + - + +
111B SER* 3.8 18.8 - - - -
112B PHE* 3.7 49.7 - - + +
114B LYS* 4.0 29.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 102 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B LEU 5.5 0.6 + - - -
98B ASP* 3.1 25.7 + - - +
99B ARG* 3.6 35.5 - - - +
100B MET 3.2 0.2 - - - -
101B LEU* 1.3 77.7 - - + +
103B SER* 1.3 61.8 + - - +
105B MET* 3.2 22.1 + - + +
106B ARG* 3.1 22.3 + - - +
200B ASN* 4.6 10.3 + - - -
201B TYR* 4.0 22.2 - - + -
267B PRO* 4.4 25.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 103 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 3.8 21.1 - - - -
75B PHE 5.5 0.6 + - - -
76B GLU* 5.4 0.3 + - - -
99B ARG* 3.0 19.6 + - - +
100B MET* 3.7 6.4 - - - -
102B ARG* 1.3 76.2 - - - +
104B ALA* 1.3 64.3 + - - +
106B ARG* 3.2 12.2 + - - +
107B LEU* 3.3 17.3 + - - +
201B TYR* 3.9 15.7 - - - +
202B LYS* 3.6 24.2 + - - +
203B LEU* 3.9 13.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B LEU* 4.2 11.4 - - + +
100B MET 2.9 14.5 + - - +
101B LEU* 3.4 13.2 - - + +
103B SER* 1.3 76.4 - - - +
105B MET* 1.3 63.3 + - + +
107B LEU* 3.1 4.3 + - - -
108B CYS 3.1 3.6 + - - -
109B LEU* 2.9 30.1 + - + +
110B PRO 4.2 12.3 - - - +
112B PHE* 4.7 4.0 - - + -
146B LEU* 3.9 25.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212A LEU* 4.2 13.5 - - - +
101B LEU* 3.1 36.9 + - + +
102B ARG* 3.2 22.4 + - + +
104B ALA* 1.3 76.8 - - + +
106B ARG* 1.3 61.9 - - - +
108B CYS* 3.3 11.2 + - - +
109B LEU 4.6 5.8 - - - +
111B SER* 4.9 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190A PHE* 5.8 1.6 - - - -
208A GLY 5.1 0.2 - - - +
209A PRO* 3.0 38.0 + - - +
212A LEU* 3.4 46.5 + - - +
213A VAL* 4.2 12.5 - - - +
102B ARG 3.1 12.2 + - - +
103B SER* 3.2 10.0 + - - +
105B MET* 1.3 78.0 - - - +
107B LEU* 1.3 61.0 + - + +
108B CYS 3.4 0.2 - - - -
197B GLY 4.5 5.7 + - - -
198B VAL* 2.9 40.2 - - + +
201B TYR* 3.5 41.1 - - + +
203B LEU* 4.7 4.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A GLY* 3.6 35.4 - - - +
209A PRO* 4.0 7.6 - - + -
211A VAL* 4.6 5.1 - - - +
71B SER 4.3 3.1 - - - +
72B LEU* 3.9 20.6 - - + +
73B GLN 3.4 41.3 - - - +
74B LEU* 4.4 7.4 - - + -
103B SER 3.3 2.6 + - - +
104B ALA 3.1 7.4 + - - +
106B ARG* 1.3 78.8 - - + +
108B CYS* 1.3 73.3 + - - +
109B LEU* 3.3 12.1 + - + +
158B PRO* 4.7 1.4 - - - +
203B LEU* 3.6 38.8 - - + -
----------------------------------------------------------
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