Contacts of the helix formed by residues 115 - 135 (chain B) in PDB entry 1N13
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 115 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B THR* 4.4 4.7 - - - -
90B SER* 3.1 8.1 + - - -
114B CYS* 1.3 76.8 - - - +
116B LYS* 1.3 65.3 + - - +
117B LYS* 3.6 11.9 + - - +
118B GLU* 3.3 20.3 + - - +
119B ALA* 3.0 19.1 + - - +
147B GLU* 3.5 13.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER* 3.2 11.7 + - - -
115B SER* 1.3 71.8 - - - +
117B LYS* 1.3 61.6 + - + +
119B ALA* 3.4 2.2 + - - +
120B GLU* 3.0 38.7 + - - +
145B ALA* 3.2 43.7 + - + +
146B VAL* 4.3 4.5 - - - -
147B GLU* 2.9 32.4 + - + +
102J SER* 5.6 5.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B SER* 3.3 10.6 + - - +
116B LYS* 1.3 81.3 - - + +
118B GLU* 1.3 62.3 + - - +
120B GLU* 3.5 5.1 + - - +
121B LYS* 3.1 25.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 4.5 8.6 + - - +
114B CYS* 3.6 26.5 - - + +
115B SER* 3.3 19.5 + - - +
117B LYS* 1.3 76.0 - - - +
119B ALA* 1.3 65.8 + - - +
121B LYS* 3.4 9.0 + - + +
122B THR* 2.9 38.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B SER* 3.8 20.0 - - - -
91B ALA 4.5 4.5 - - - +
92B ALA* 3.7 15.3 - - + +
110B TYR* 3.7 25.5 - - + -
114B CYS* 3.9 4.0 - - - -
115B SER 3.0 16.8 + - - +
116B LYS* 3.8 3.8 - - - +
118B GLU* 1.3 77.4 - - - +
120B GLU* 1.3 57.3 + - - +
122B THR* 3.3 2.6 + - - -
123B VAL* 3.0 31.0 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
92B ALA* 3.9 3.3 - - - +
116B LYS* 3.0 27.3 + - - +
117B LYS* 4.0 4.8 - - - +
119B ALA* 1.3 75.5 - - - +
121B LYS* 1.3 62.5 + - - +
123B VAL* 3.4 7.2 - - + +
124B ARG* 3.1 33.4 + - - +
143B SER* 2.7 43.5 + - - +
144B ILE* 4.3 2.9 - - - +
145B ALA* 3.7 19.6 + - + +
66H LYS* 3.3 32.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LYS 3.1 19.2 + - - +
118B GLU* 3.7 9.0 - - + +
120B GLU* 1.3 75.8 - - - +
122B THR* 1.3 65.7 + - - +
124B ARG* 3.5 7.8 + - - +
125B GLU* 3.1 24.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B TYR* 3.8 36.9 + - + -
118B GLU* 2.9 27.6 + - - +
119B ALA 3.7 3.4 - - - -
121B LYS* 1.3 80.3 - - - +
123B VAL* 1.3 58.1 + - - +
125B GLU* 3.2 8.6 + - + +
126B MET* 2.9 39.5 + - + +
29C THR* 5.7 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92B ALA* 3.7 26.9 - - + +
93B ILE 3.9 7.0 - - - +
94B SER* 2.7 32.5 + - - +
108B MET* 3.3 36.3 - - + +
109B GLU 3.8 9.6 - - - +
110B TYR* 3.8 8.2 - - + +
119B ALA 3.0 15.6 + - - +
120B GLU* 3.4 12.6 - - - +
122B THR* 1.3 73.9 - - - +
124B ARG* 1.3 67.0 + - + +
126B MET* 3.3 9.0 + - - +
127B ALA 3.2 12.6 + - - -
143B SER* 4.7 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 4.0 5.6 - - - -
120B GLU* 3.1 33.8 + - - +
121B LYS* 3.9 7.0 - - - +
123B VAL* 1.3 73.0 - - - +
125B GLU* 1.3 66.0 + - - +
127B ALA* 3.2 2.3 + - - +
128B LYS* 3.1 18.6 + - - +
141B ILE* 2.8 66.4 + - + +
143B SER* 2.9 38.5 + - - +
64H LEU 4.8 3.4 + - - -
65H PRO 4.7 2.4 - - - -
66H LYS* 3.6 51.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B LYS* 3.1 16.0 + - + +
122B THR* 3.2 11.2 + - + +
124B ARG* 1.3 78.0 - - - +
126B MET* 1.3 56.7 + - + +
128B LYS* 3.2 39.4 + - - +
129B ILE* 2.9 54.9 + - + +
28C GLU* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B MET* 3.8 14.6 - - + +
109B GLU 3.8 14.6 - - - +
110B TYR* 4.0 27.6 - - + -
122B THR* 2.9 25.8 + - + +
123B VAL* 3.5 14.6 - - - +
124B ARG 3.2 0.6 - - - -
125B GLU* 1.3 77.7 - - + +
127B ALA* 1.3 61.6 + - - +
129B ILE* 3.4 3.2 + - + -
130B GLY* 3.1 8.1 + - - -
29C THR* 3.7 24.2 - - + +
31C LEU* 3.6 34.1 - - + -
32C ASN* 3.0 37.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B SER* 3.4 26.5 - - - +
96B ALA* 3.8 28.8 - - + +
106B LEU* 3.8 9.9 - - - +
108B MET* 3.7 12.3 - - + +
123B VAL 3.2 4.9 + - - -
124B ARG 3.2 7.4 + - - +
126B MET* 1.3 74.0 - - - +
128B LYS* 1.3 67.5 + - - +
130B GLY* 3.1 2.8 + - - -
131B PHE* 3.1 21.1 + - - +
141B ILE* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ARG 3.1 12.2 + - - +
125B GLU* 3.3 38.5 + - - +
127B ALA* 1.3 76.8 - - - +
129B ILE* 1.3 61.0 - - - +
131B PHE* 3.1 6.4 + - - +
132B GLU* 2.8 57.9 + - + +
138B LEU* 4.6 15.9 - - + +
141B ILE* 4.0 14.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B GLU* 2.9 43.7 + - + +
126B MET* 3.6 8.3 - - + +
128B LYS* 1.3 75.7 - - - +
130B GLY* 1.3 54.7 + - - +
132B GLU* 3.0 17.6 + - - +
133B MET* 2.9 43.5 + - + +
28C GLU* 3.4 48.0 - - + +
29C THR* 5.3 3.4 - - + -
32C ASN* 3.6 31.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106B LEU* 3.4 22.0 - - - -
126B MET 3.1 12.2 + - - -
127B ALA 3.1 0.8 + - - -
129B ILE* 1.3 75.5 - - - +
131B PHE* 1.3 60.9 + - - +
133B MET* 3.4 8.0 + - - +
134B ARG* 3.1 38.3 + - - +
32C ASN* 4.3 4.9 - - - -
35C ASP* 4.0 6.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B ALA* 3.6 31.9 - - + -
97B ILE 4.0 4.0 - - - -
98B PRO* 3.5 38.4 - - + -
104B CYS 3.6 20.4 - - - -
106B LEU* 3.8 21.3 - - + -
127B ALA 3.1 6.5 + - - +
128B LYS 3.1 9.4 + - - +
130B GLY* 1.3 75.0 - - - +
132B GLU* 1.3 60.1 + - - +
134B ARG* 3.2 5.8 + - - -
135B GLY 2.9 22.5 + - - -
136B TRP* 3.1 54.1 + + + +
137B GLU 3.8 4.9 - - - -
138B LEU* 3.8 26.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128B LYS* 2.8 55.5 + - + +
129B ILE* 3.0 22.3 + - - +
131B PHE* 1.3 75.8 - - + +
133B MET* 1.3 62.4 + - + +
135B GLY* 3.1 14.2 + - - +
136B TRP 5.5 0.4 - - - -
28C GLU* 4.8 4.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ILE* 2.9 38.0 + - + +
130B GLY* 3.7 10.5 - - - +
132B GLU* 1.3 79.6 - - + +
134B ARG* 1.3 59.0 + - - +
135B GLY 3.7 0.2 + - - -
25C SER* 3.9 12.1 - - - +
26C GLU 3.9 8.3 - - - +
27C GLY* 5.1 2.7 - - - -
32C ASN* 3.6 30.3 - - - +
35C ASP* 5.1 2.7 - - - +
36C GLY* 3.7 22.0 - - - -
39C LEU* 4.6 11.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54B ILE* 4.1 2.6 - - - +
106B LEU* 3.7 21.8 - - - +
130B GLY 3.1 24.5 + - - +
131B PHE* 3.2 8.5 + - - +
132B GLU 3.2 0.2 - - - -
133B MET* 1.3 77.6 - - - +
135B GLY* 1.3 63.6 + - - +
136B TRP* 3.3 54.1 + - + +
7011B AG2 3.8 2.2 + - - -
35C ASP* 2.7 42.8 + - - -
39C LEU* 3.7 25.1 - - + +
44C GLY 3.0 24.2 + - - -
45C ASN* 2.8 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE 2.9 6.0 + - - -
132B GLU* 3.1 13.5 + - - -
133B MET 3.3 0.4 + - - -
134B ARG* 1.3 79.8 - - - +
136B TRP* 1.3 64.3 + - - +
137B GLU* 4.2 1.4 + - - +
----------------------------------------------------------
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