Contacts of the helix formed by residues 97 - 113 (chain E) in PDB entry 6H25
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 GLY 97 (chain E).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92E GLU 5.3 0.9 - - - -
93E PHE* 3.6 20.9 - - - +
94E GLU 4.7 0.4 - - - +
95E GLY 4.5 2.6 - - - +
96E ARG* 1.3 77.8 - - - +
98E GLY* 1.3 63.7 + - - +
100E ASP* 3.4 20.3 + - - +
101E LEU* 3.8 6.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 98 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E VAL 5.4 0.2 - - - +
85E CYS* 3.3 36.9 + - - +
93E PHE* 3.4 16.9 - - - +
94E GLU 5.6 0.6 - - - -
95E GLY 5.2 0.8 - - - -
96E ARG* 3.2 2.2 - - - +
97E GLY* 1.3 79.6 - - - +
99E ASP* 1.3 60.2 + - - +
101E LEU 3.7 0.2 + - - -
102E GLY* 2.9 26.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 99 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B PRO* 4.1 30.3 - - - +
82E PHE* 5.1 6.8 - - - -
83E VAL 5.2 3.8 - - - +
84E ASP* 4.8 9.7 - - - +
85E CYS 5.7 0.3 + - - -
95E GLY 4.8 8.9 - - - +
96E ARG* 3.5 11.6 + - - +
97E GLY 3.3 0.8 - - - -
98E GLY* 1.3 75.4 - - - +
100E ASP* 1.3 56.5 + - - +
102E GLY* 4.6 2.0 - - - +
103E THR* 2.3 35.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 100 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96E ARG 4.0 3.1 + - - +
97E GLY* 3.4 17.3 + - - +
98E GLY 3.1 0.8 - - - -
99E ASP* 1.3 76.1 - - - +
101E LEU* 1.3 62.0 + - - +
103E THR* 3.0 27.2 + - - -
104E GLU* 3.5 5.5 + - - +
120F ARG* 5.4 7.7 - - - +
124F LEU* 5.3 8.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85E CYS* 3.7 26.9 - - + -
93E PHE* 5.3 12.3 - - + -
97E GLY 3.8 5.3 + - - +
98E GLY 3.7 3.0 + - - +
100E ASP* 1.3 79.0 - - - +
102E GLY* 1.3 58.4 + - - +
104E GLU* 3.0 29.3 + - - +
105E ILE* 3.4 33.8 + - + +
141E LEU* 5.7 0.7 - - + -
148E LEU* 4.1 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 102 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E VAL* 3.5 44.5 + - - +
85E CYS* 4.0 10.1 - - - -
98E GLY 2.9 19.7 + - - -
99E ASP* 4.2 1.8 - - - -
101E LEU* 1.3 76.4 - - - +
103E THR* 1.3 65.3 + - - +
105E ILE* 4.6 0.9 - - - -
106E ALA* 3.7 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 103 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99E ASP 2.3 26.3 + - - -
100E ASP* 3.0 10.9 + - - -
102E GLY* 1.3 76.9 - - - +
104E GLU* 1.3 65.2 + - - +
106E ALA* 3.0 17.6 + - - +
107E ASN* 3.1 32.5 + - - +
116F GLY 5.0 6.7 - - - +
117F CYS* 5.1 1.8 - - - +
120F ARG* 4.4 31.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 104 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100E ASP 3.5 4.2 + - - +
101E LEU* 3.0 17.2 + - - +
103E THR* 1.3 78.9 - - - +
105E ILE* 1.3 64.3 + - + +
107E ASN* 3.0 23.7 + - + +
108E THR* 3.1 13.3 + - + +
149E PHE* 4.9 10.9 - - + -
240E ARG* 2.9 41.1 + - - +
242E VAL* 4.8 6.8 - - - +
124F LEU* 4.1 26.2 - - + +
128F GLU* 4.4 6.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 105 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83E VAL* 4.0 26.5 - - + -
101E LEU* 3.4 36.5 + - + +
104E GLU* 1.3 75.6 - - + +
106E ALA* 1.3 63.2 + - - +
108E THR* 2.3 29.7 + - - -
109E LEU* 3.2 22.4 + - + +
141E LEU* 5.4 2.9 - - + -
148E LEU* 3.9 19.1 - - + -
149E PHE* 3.7 27.6 - - + -
152E ILE* 3.8 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 106 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E PHE* 4.6 17.3 - - + +
82E PHE* 5.0 0.7 - - - -
83E VAL* 4.2 22.2 - - + +
102E GLY 3.7 12.4 + - - +
103E THR* 3.0 11.7 + - - +
105E ILE* 1.3 77.6 - - - +
107E ASN* 1.3 65.2 + - - +
109E LEU* 3.0 18.6 + - - +
110E TYR* 3.2 22.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 107 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103E THR* 3.1 37.3 + - - +
104E GLU* 3.0 12.4 + - + +
106E ALA* 1.3 76.7 - - - +
108E THR* 1.3 63.9 + - + +
110E TYR* 3.1 31.8 + - - +
111E ARG* 3.4 10.2 + - - +
240E ARG* 6.2 0.2 - - - +
117F CYS* 3.4 18.9 + - - +
118F GLU* 5.6 1.6 - - - +
120F ARG 5.0 0.4 - - - -
121F GLU* 3.7 43.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 108 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E GLU 3.1 10.9 + - - +
105E ILE* 2.3 28.2 + - - -
107E ASN* 1.3 75.8 - - + +
109E LEU* 1.3 70.2 + - - +
111E ARG* 3.0 15.4 + - - +
112E ILE* 3.0 34.3 + - - +
149E PHE* 4.1 18.6 - - + -
200E ILE* 4.9 2.9 - - - +
227E LEU* 5.7 6.3 - - + -
240E ARG* 3.4 36.1 - - - +
121F GLU* 6.5 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 109 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E PHE* 3.6 43.1 - - + -
83E VAL* 5.5 3.1 - - + -
105E ILE* 3.3 33.0 - - + +
106E ALA 3.0 10.8 + - - +
108E THR* 1.3 88.3 + - - +
110E TYR* 1.3 56.1 + - - +
112E ILE* 3.1 8.6 + - + -
113E PHE* 2.8 39.6 + - + -
139E VAL* 4.7 9.9 - - + -
149E PHE* 5.7 1.1 - - + -
152E ILE* 4.4 21.3 - - + -
153E SER* 5.5 2.5 - - - +
156E VAL* 4.9 12.3 - - + -
200E ILE* 5.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 110 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU 4.3 17.7 - - - -
80E GLU* 2.9 29.7 + - - -
81E PHE* 3.5 36.1 + + + -
106E ALA* 3.2 33.3 + - + -
107E ASN* 3.1 19.3 + - - +
109E LEU* 1.3 74.8 - - - +
111E ARG* 1.3 52.3 + - + +
113E PHE* 2.9 7.8 - - - +
114E ASN* 2.7 39.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 111 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107E ASN 3.4 9.6 + - - +
108E THR* 3.0 14.7 + - - +
110E TYR* 1.3 78.3 - - + +
112E ILE* 1.3 61.5 + - - +
114E ASN* 3.0 23.5 + - + +
115E ASN* 4.7 1.4 - - - +
237E THR* 5.2 2.1 - - - -
238E CYS* 3.6 26.4 - - + +
240E ARG* 6.5 0.2 - - - +
118F GLU* 4.6 7.1 + - - -
121F GLU* 2.8 42.8 + - - +
122F LEU* 4.7 5.5 - - - +
226F LEU* 3.5 33.0 - - - +
227F GLY* 4.7 0.6 - - - -
228F SER* 3.4 43.6 + - - +
229F GLY 4.7 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108E THR* 3.0 32.0 + - - +
109E LEU* 3.5 10.1 - - + +
111E ARG* 1.3 74.6 - - - +
113E PHE* 1.3 83.5 + - + +
115E ASN* 3.1 23.6 + - - -
118E SER* 4.1 1.2 + - - -
153E SER* 6.0 1.1 - - - +
198E PRO* 3.7 28.2 - - + +
200E ILE* 3.7 32.3 - - + -
227E LEU* 5.3 2.9 - - + -
229E SER* 3.9 23.8 - - - +
237E THR* 4.3 6.2 + - - +
238E CYS* 3.7 18.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 113 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E LEU* 4.2 20.9 - - + -
81E PHE* 3.4 35.0 - + + -
109E LEU* 2.8 30.8 + - + +
110E TYR* 2.9 6.8 - - - +
112E ILE* 1.3 93.7 - - + +
114E ASN* 1.3 53.8 + - - -
115E ASN 3.3 7.7 + - - +
116E LYS 5.3 0.2 + - - -
118E SER* 3.2 32.4 - - - -
119E VAL* 4.4 8.3 - - + -
156E VAL* 4.8 17.7 - - + -
160E LEU* 4.5 12.6 - - + -
197E VAL* 3.7 31.4 - - + -
198E PRO* 4.7 1.6 - - + -
----------------------------------------------------------
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