Contacts of the helix formed by residues 103 - 118 (chain B) in PDB entry 2AWP
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 SER 103 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 4.0 7.2 + - - -
98B GLN* 4.4 10.1 - - - +
101B PHE* 3.2 6.3 + - - +
102B GLY* 1.3 78.5 - - - +
104B PHE* 1.3 63.1 + - - +
105B ASN* 3.5 10.4 + - - +
106B ASN* 3.1 29.5 + - - +
107B PHE* 3.1 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 104 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY 3.8 22.4 - - - -
88B GLU* 3.6 33.7 - - - +
89B PRO* 3.5 26.7 - - + -
97B ILE* 3.8 12.3 - - + +
98B GLN* 4.8 6.8 - - + +
103B SER* 1.3 71.7 - - - +
105B ASN* 1.3 59.0 + - - +
107B PHE* 3.2 11.8 + + - +
108B LYS* 2.7 57.3 + - + +
180B TRP* 3.9 26.2 - + + -
185B TRP* 3.5 26.2 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 105 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103B SER* 3.3 9.3 + - - +
104B PHE* 1.3 81.4 - - - +
106B ASN* 1.3 64.3 + - - +
108B LYS* 3.8 10.1 - - - +
109B ASN* 3.0 59.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 3.2 28.1 + - + +
102B GLY* 4.4 4.0 - - - -
103B SER* 3.1 22.9 + - - +
105B ASN* 1.3 83.9 - - - +
107B PHE* 1.3 61.7 + - - +
109B ASN* 4.0 5.8 + - - +
110B GLU* 3.1 25.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 107 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.7 40.6 - - + -
101B PHE* 3.6 31.9 - + + +
103B SER 3.1 6.8 + - - +
104B PHE* 3.2 15.9 + + - +
106B ASN* 1.3 75.5 - - - +
108B LYS* 1.3 55.8 + - - +
110B GLU* 3.2 3.4 + - - +
111B PHE* 2.7 55.2 + + + +
126B LEU* 3.8 31.9 - - + -
136B ILE* 3.7 28.5 - - + -
155B LEU* 5.4 3.8 - - + -
180B TRP* 3.6 22.4 - + - -
185B TRP* 4.2 7.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 108 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B PHE* 2.7 49.6 + - + +
105B ASN* 3.8 10.3 - - - +
107B PHE* 1.3 72.6 - - - +
109B ASN* 1.3 64.8 + - - +
112B SER* 2.8 36.8 + - - +
177B LYS* 6.5 0.4 - - - -
180B TRP* 3.6 56.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 109 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B ASN* 3.0 48.6 + - - +
106B ASN* 4.0 5.3 + - - +
108B LYS* 1.3 81.8 - - - +
110B GLU* 1.3 57.5 + - - +
112B SER* 3.4 5.7 + - - -
113B ASN* 2.9 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B PHE* 5.8 2.9 - - + -
106B ASN 3.1 17.8 + - - +
107B PHE* 4.0 2.2 - - - +
109B ASN* 1.3 72.9 - - - +
111B PHE* 1.3 67.8 + - - +
113B ASN* 3.1 20.4 + - - +
114B VAL* 3.0 36.8 + - + +
136B ILE* 3.7 19.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 111 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107B PHE* 2.7 34.9 + + + +
110B GLU* 1.3 70.3 - - - +
112B SER* 1.3 62.0 + - - +
114B VAL* 3.3 5.4 + - + +
115B LEU* 2.9 48.6 + - + +
124B GLY* 3.6 28.3 - - - -
125B TRP* 3.5 34.3 - - - -
126B LEU* 4.2 4.5 - - + -
136B ILE* 3.6 31.4 - - + +
155B LEU* 5.1 4.3 - - + -
156B THR 5.3 0.2 - - - -
157B CYS* 4.5 3.1 - - + -
179B TRP* 3.9 20.0 - + - -
180B TRP* 3.7 28.0 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 112 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LYS* 2.8 26.4 + - - +
109B ASN* 3.6 7.1 - - - -
111B PHE* 1.3 77.0 - - - +
113B ASN* 1.3 63.3 + - - +
115B LEU* 3.4 1.1 + - - +
116B CYS* 3.0 32.9 + - - -
176B VAL* 3.7 18.0 - - - +
177B LYS* 5.8 0.3 - - - -
180B TRP* 3.0 23.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 113 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B ASN* 2.9 23.5 + - - +
110B GLU* 3.1 23.3 + - - +
112B SER* 1.3 77.1 - - - +
114B VAL* 1.3 59.8 + - + +
116B CYS* 3.3 5.2 + - - +
117B GLY* 2.9 27.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 114 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLU* 3.0 33.8 + - - +
111B PHE* 3.7 7.9 - - + +
113B ASN* 1.3 76.1 - - + +
115B LEU* 1.3 63.7 + - - +
117B GLY* 3.2 9.9 + - - -
118B HIS* 3.4 14.7 + - - +
124B GLY* 5.0 5.6 - - - -
136B ILE* 3.8 28.5 - - + -
137B LEU 4.3 4.0 - - - +
138B GLN* 3.8 40.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 115 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111B PHE* 2.9 48.3 + - + +
112B SER* 3.8 2.9 - - - +
114B VAL* 1.3 76.1 - - - +
116B CYS* 1.3 58.7 + - - +
118B HIS* 3.8 1.0 + - - -
124B GLY* 3.5 36.1 - - - +
157B CYS* 3.7 32.8 - - + +
159B ILE* 3.6 18.0 - - + +
172B ARG* 2.9 28.9 + - - -
176B VAL* 3.8 31.0 - - + -
179B TRP* 4.7 6.3 - - + -
180B TRP* 5.1 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B SER* 3.0 27.7 + - - +
113B ASN* 3.9 4.3 - - - +
115B LEU* 1.3 77.5 - - - +
117B GLY* 1.3 61.1 + - - +
118B HIS 4.5 0.2 - - - +
172B ARG* 3.5 18.0 + - - +
173B PRO* 3.7 43.1 - - + -
176B VAL* 4.0 16.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASN 2.9 16.1 + - - -
114B VAL* 3.2 3.9 + - - -
116B CYS* 1.3 77.9 - - - +
118B HIS* 1.3 63.5 + - - +
119B PHE* 3.3 5.7 + - - +
138B GLN* 5.0 1.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B VAL 3.4 10.4 + - - +
115B LEU* 4.2 0.9 - - - +
116B CYS 3.3 2.4 - - - -
117B GLY* 1.3 77.0 - - - +
119B PHE* 1.3 75.7 + - - +
120B GLY 3.8 5.3 - - - +
121B SER 3.5 6.5 + - - -
122B GLY* 4.0 0.7 - - - -
123B TRP 5.1 1.6 - - - +
138B GLN* 2.7 40.4 + - + +
139B THR 3.2 26.6 + - - -
140B HIS* 2.9 30.1 + - + -
159B ILE* 3.6 31.6 - - + -
172B ARG* 2.7 34.1 + - - +
----------------------------------------------------------
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