Contacts of the helix formed by residues 131 - 145 (chain G) in PDB entry 1N34
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 LYS 131 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126G ASP* 3.4 41.1 + - - +
129G GLU* 3.1 36.7 + - + +
130G GLY* 1.3 82.4 - - - +
132G GLY* 1.3 58.2 + - - +
133G GLY 4.2 0.5 + - - -
139G GLU* 5.5 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G GLU* 4.0 4.0 - - - -
126G ASP* 3.3 18.9 + - - -
127G ALA* 4.6 1.3 - - - -
130G GLY 3.9 0.4 - - - -
131G LYS* 1.3 78.9 - - - +
133G GLY* 1.3 68.2 + - - -
134G ALA* 2.9 3.6 - - - -
135G VAL* 2.7 29.8 + - - +
136G LYS* 2.7 13.4 + - - +
139G GLU* 5.4 0.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ALA* 3.5 20.4 - - - +
111G ARG* 6.1 1.2 - - - +
123G GLU* 3.2 14.4 + - - -
126G ASP* 5.5 0.6 - - - +
131G LYS 4.2 1.2 + - - -
132G GLY* 1.3 70.5 - - - +
134G ALA* 1.3 64.0 + - - +
136G LYS* 3.2 18.7 - - - +
137G LYS* 3.5 7.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G VAL* 3.7 16.8 - - + +
103G TRP* 3.9 16.9 - - - +
104G LEU* 3.4 35.7 - - + +
107G ALA* 3.6 7.2 - - - +
123G GLU* 3.5 8.4 + - - +
127G ALA* 6.5 0.7 - - - -
132G GLY 2.7 3.4 + - - -
133G GLY* 1.3 69.2 - - - +
135G VAL* 1.3 54.8 + - + +
136G LYS 2.5 16.4 + - - -
137G LYS* 2.6 20.9 + - - +
138G LYS 2.9 9.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN* 4.1 18.2 - - + +
69G VAL* 4.0 19.3 - - + +
127G ALA* 3.9 24.2 - - - +
130G GLY* 4.9 9.6 - - - +
131G LYS 5.3 0.7 - - - +
132G GLY* 2.7 25.1 + - - +
134G ALA* 1.3 71.0 - - + +
136G LYS* 1.3 55.7 + - - +
138G LYS* 3.6 25.8 - - + -
139G GLU* 2.8 62.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G GLY 2.7 10.0 + - - +
133G GLY* 3.2 14.4 - - - +
134G ALA 2.5 4.9 + - - -
135G VAL* 1.3 71.3 - - - +
137G LYS* 1.3 78.9 + - - +
139G GLU* 2.9 10.5 + - - +
140G ASP* 2.4 74.3 + - + +
143G ARG* 5.7 6.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 137 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G TRP* 3.5 34.8 - - + +
106G GLN* 2.8 34.7 - - - +
107G ALA* 4.3 18.7 - - + +
110G GLN* 5.2 10.7 - - - +
133G GLY 4.0 8.7 - - - +
134G ALA* 2.6 11.1 + - - +
136G LYS* 1.3 88.7 - - - +
138G LYS* 1.3 55.7 + - - +
140G ASP* 3.7 8.3 - - - -
141G VAL* 2.5 40.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 138 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68G ASN 3.1 15.9 - - - +
69G VAL* 3.0 33.7 - - + +
71G PRO* 4.4 9.1 - - + +
72G ARG* 2.9 23.9 - - - +
103G TRP* 4.4 7.9 - - + -
134G ALA 2.9 6.1 + - - +
135G VAL* 3.4 21.3 - - + +
137G LYS* 1.3 74.8 - - - +
139G GLU* 1.3 92.8 + - + +
141G VAL* 2.9 9.7 - - - +
142G GLU* 2.7 75.6 + - - +
143G ARG* 5.6 0.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 139 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130G GLY* 4.1 15.5 - - - +
131G LYS* 5.5 0.2 - - - -
132G GLY 5.4 0.2 + - - -
135G VAL* 2.8 47.3 + - + +
136G LYS* 3.3 5.8 + - + +
138G LYS* 1.3 99.3 - - + +
140G ASP* 1.3 56.7 + - - +
142G GLU* 4.1 0.2 - - - -
143G ARG* 2.5 71.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 140 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G LYS* 2.4 63.0 + - + +
137G LYS* 3.2 4.8 - - - +
139G GLU* 1.3 71.5 - - - +
141G VAL* 1.3 64.9 + - - +
143G ARG* 3.3 12.9 + - - +
144G MET* 3.1 30.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 141 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PRO* 5.0 4.7 - - + -
73G MET 5.0 0.4 - - - +
74G GLU* 4.0 32.1 - - + +
75G VAL* 5.3 1.3 - - + +
103G TRP* 3.7 26.5 - - + -
137G LYS* 2.5 20.5 + - + +
138G LYS* 2.9 21.1 - - - +
140G ASP* 1.3 76.3 + - - +
142G GLU* 1.3 75.8 + - + +
144G MET* 2.8 30.6 - - + +
145G ALA 3.8 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 142 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71G PRO* 3.4 5.4 - - + +
72G ARG* 2.6 64.0 + - - +
73G MET* 4.3 22.2 - - + +
138G LYS* 2.7 43.8 + - - +
139G GLU* 3.4 2.5 - - - +
141G VAL* 1.3 75.0 - - + +
143G ARG* 1.3 56.3 + - + +
144G MET 2.7 0.2 + - - -
145G ALA* 2.6 39.2 + - - +
146G GLU* 4.8 6.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 143 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136G LYS* 5.7 6.1 - - - +
138G LYS* 5.6 0.7 - - - +
139G GLU* 2.5 60.0 + - + +
140G ASP* 3.7 11.9 + - - +
142G GLU* 1.3 77.0 - - + +
144G MET* 1.3 56.4 + - - +
145G ALA 2.4 20.1 - - - +
146G GLU* 5.3 3.4 - - - -
147G ALA* 3.3 10.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 144 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G VAL* 4.4 18.6 - - + -
140G ASP* 3.1 23.0 + - - +
141G VAL* 2.8 31.5 + - + +
142G GLU 2.7 3.4 + - - -
143G ARG* 1.3 72.5 - - - +
145G ALA* 1.3 55.0 + - - +
147G ALA* 3.0 12.5 - - - +
148G ASN* 2.6 30.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 145 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73G MET* 3.8 37.0 - - + -
74G GLU* 4.3 10.5 - - - +
75G VAL* 5.0 1.8 - - + +
88G PRO* 4.2 14.1 - - + -
142G GLU 2.6 16.3 + - - +
143G ARG 2.4 27.0 - - - +
144G MET* 1.3 71.7 - - - +
146G GLU* 1.3 66.6 + - + +
147G ALA 2.6 12.7 + - - +
148G ASN* 4.3 3.8 - - - +
----------------------------------------------------------
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