Contacts of the helix formed by residues 115 - 135 (chain H) 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 H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88H THR* 4.5 4.3 - - - -
90H SER* 3.2 8.8 + - - -
114H CYS* 1.3 74.8 - - - +
116H LYS* 1.3 64.0 + - - +
117H LYS* 3.6 12.5 + - - +
118H GLU* 3.3 25.5 + - - +
119H ALA* 3.0 21.1 + - - +
147H GLU* 3.6 11.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 116 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B LYS* 5.8 9.9 - - - -
90H SER* 3.3 11.9 + - - -
115H SER* 1.3 72.2 - - - +
117H LYS* 1.3 64.3 + - - +
119H ALA* 3.4 0.9 + - - +
120H GLU* 3.0 41.1 + - - +
144H ILE* 5.8 0.2 - - - +
145H ALA* 3.1 42.4 + - + +
146H VAL* 3.9 5.2 - - - +
147H GLU* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115H SER* 3.2 11.1 + - - +
116H LYS* 1.3 81.3 - - - +
118H GLU* 1.3 76.2 + - - +
120H GLU* 3.4 5.8 + - - +
121H LYS* 3.1 25.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 118 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114H CYS* 4.2 17.9 - - + -
115H SER* 3.3 20.5 + - - +
117H LYS* 1.3 93.6 - - - +
119H ALA* 1.3 65.1 + - - +
121H LYS* 3.4 31.4 + - - +
122H THR* 3.0 32.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 119 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90H SER* 3.7 21.5 - - - -
91H ALA 4.6 4.0 - - - +
92H ALA* 3.6 19.5 - - + +
110H TYR* 3.8 25.4 - - + -
114H CYS* 3.9 4.6 - - - -
115H SER 3.0 16.6 + - - +
116H LYS* 3.7 4.3 - - - +
118H GLU* 1.3 78.2 - - - +
120H GLU* 1.3 58.0 + - - +
122H THR* 3.4 2.4 + - - -
123H VAL* 3.0 25.1 + - - +
145H ALA* 4.7 0.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 120 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ALA* 4.0 2.9 - - - +
116H LYS* 3.0 33.4 + - - +
117H LYS* 3.9 5.8 - - - +
119H ALA* 1.3 72.9 - - - +
121H LYS* 1.3 65.6 + - - +
123H VAL* 3.4 7.0 - - + +
124H ARG* 3.0 38.7 + - - +
143H SER* 2.7 46.0 + - - +
144H ILE* 3.8 8.5 + - - +
145H ALA* 3.8 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117H LYS* 3.1 19.3 + - + +
118H GLU* 3.6 33.9 + - - +
119H ALA 3.3 0.2 - - - -
120H GLU* 1.3 76.2 - - - +
122H THR* 1.3 67.0 + - - +
124H ARG* 3.4 8.3 + - - +
125H GLU* 3.1 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 122 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110H TYR* 3.7 40.7 + - + +
118H GLU* 3.0 20.5 + - - +
119H ALA 3.7 4.5 - - - -
121H LYS* 1.3 81.3 + - - +
123H VAL* 1.3 56.9 + - - +
125H GLU* 3.2 17.0 + - - +
126H MET* 3.0 35.9 + - + +
29K THR* 5.6 5.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 123 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92H ALA* 3.6 26.9 - - + +
93H ILE 4.0 5.8 - - - +
94H SER* 2.8 31.7 + - - +
108H MET* 3.3 35.4 - - + +
109H GLU* 3.8 17.3 - - - +
110H TYR* 3.9 7.0 - - + -
119H ALA 3.0 10.8 + - - +
120H GLU* 3.4 12.6 - - - +
122H THR* 1.3 76.2 - - - +
124H ARG* 1.3 67.8 + - + +
126H MET* 3.4 8.9 + - - +
127H ALA 3.2 12.5 + - - -
143H SER* 4.5 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 124 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H SER* 4.2 5.4 - - - -
120H GLU* 3.0 34.0 + - - +
121H LYS* 3.7 7.0 - - - +
123H VAL* 1.3 75.2 - - - +
125H GLU* 1.3 63.7 + - + +
127H ALA* 3.3 1.9 + - - +
128H LYS* 3.1 18.0 + - - +
141H ILE* 2.9 64.9 + - + +
143H SER* 2.9 41.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 125 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121H LYS* 3.1 49.1 + - + +
122H THR* 3.4 16.2 + - - +
124H ARG* 1.3 77.4 - - + +
126H MET* 1.3 56.8 + - + +
128H LYS* 3.2 10.3 + - - +
129H ILE* 2.9 41.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 126 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108H MET* 3.8 13.6 - - + +
109H GLU 3.5 21.3 - - - +
110H TYR* 4.0 15.7 - - + -
122H THR* 3.0 36.1 + - + +
123H VAL* 3.6 13.7 - - - +
124H ARG 3.3 0.2 - - - -
125H GLU* 1.3 77.4 - - + +
127H ALA* 1.3 61.1 - - - +
129H ILE* 3.4 3.5 + - + -
130H GLY* 3.1 8.7 + - - -
29K THR* 3.8 23.1 - - + +
31K LEU* 3.6 30.7 - - + -
32K ASN* 3.0 38.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 127 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94H SER* 3.4 26.2 - - - +
96H ALA* 4.0 32.3 - - + +
106H LEU* 3.7 11.1 - - - +
108H MET* 3.7 13.2 - - + +
123H VAL 3.2 5.7 + - - -
124H ARG 3.7 6.5 - - - +
125H GLU 3.3 0.2 - - - -
126H MET* 1.3 73.6 - - - +
128H LYS* 1.3 65.3 + - - +
130H GLY* 3.1 10.7 + - - -
131H PHE* 3.2 9.0 + - - +
141H ILE* 4.3 4.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 128 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ALA* 5.4 0.4 - - - -
124H ARG 3.1 13.4 + - - +
125H GLU* 3.2 11.6 + - - +
127H ALA* 1.3 77.4 - - - +
129H ILE* 1.3 61.2 + - + +
131H PHE* 3.1 8.6 + - - +
132H GLU* 3.0 40.8 + - - +
138H LEU* 4.7 14.4 - - + -
141H ILE* 4.0 17.6 - - + +
7007H MRD 4.1 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 129 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125H GLU* 2.9 29.7 + - + +
126H MET* 3.6 7.4 - - + +
127H ALA 3.3 0.2 - - - -
128H LYS* 1.3 75.4 - - + +
130H GLY* 1.3 55.9 + - - +
132H GLU* 3.1 20.0 + - - +
133H MET* 2.9 43.4 + - + +
28K GLU* 3.7 46.2 - - + +
29K THR* 5.2 2.7 - - + -
32K ASN* 3.6 31.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106H LEU* 3.3 23.6 - - - -
126H MET 3.1 11.3 + - - -
127H ALA 3.1 1.0 + - - -
129H ILE* 1.3 78.6 - - - +
131H PHE* 1.3 58.4 + - - +
133H MET* 3.5 6.1 + - - +
134H ARG* 3.1 38.7 + - - +
32K ASN* 4.4 4.7 - - - -
35K ASP* 4.0 6.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 131 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96H ALA* 3.5 37.7 - - + -
98H PRO* 3.6 34.8 - - + -
104H CYS 3.8 11.9 - - - -
106H LEU* 3.7 24.9 - - + -
127H ALA 3.2 6.8 + - - +
128H LYS* 3.1 11.2 + - - +
130H GLY* 1.3 74.4 - - - +
132H GLU* 1.3 55.5 + - - +
134H ARG* 3.3 4.5 + - - -
135H GLY 2.8 29.3 + - - -
136H TRP* 3.0 49.5 + + + +
137H GLU 3.6 6.7 - - - -
138H LEU* 3.8 22.2 - - + -
7007H MRD 3.7 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 132 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128H LYS* 3.0 42.2 + - + +
129H ILE* 3.1 24.4 + - + +
131H PHE* 1.3 77.2 - - - +
133H MET* 1.3 63.6 + - + +
135H GLY* 3.2 12.5 + - - -
7007H MRD 3.2 31.4 - - + +
28K GLU* 4.4 7.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 133 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129H ILE* 2.9 38.1 + - + +
130H GLY* 3.8 9.4 - - - +
131H PHE 3.3 0.2 - - - -
132H GLU* 1.3 79.0 - - + +
134H ARG* 1.3 58.9 + - - +
135H GLY 3.8 0.2 + - - -
25K SER* 4.2 9.4 - - - +
26K GLU 4.2 7.6 - - - +
27K GLY* 5.6 2.5 - - - -
32K ASN* 3.7 20.4 - - - +
35K ASP* 5.0 2.9 - - - +
36K GLY* 3.5 32.3 - - - -
39K LEU* 4.7 13.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 134 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H ILE* 4.1 2.1 - - - +
104H CYS* 5.4 0.2 - - - -
106H LEU* 3.7 18.7 - - - +
130H GLY 3.1 25.0 + - - +
131H PHE* 3.3 8.2 + - - +
132H GLU 3.2 0.4 - - - -
133H MET* 1.3 77.8 - - - +
135H GLY* 1.3 62.8 + - - +
136H TRP* 3.3 53.4 + - + +
7012H AG2 3.9 1.0 + - - -
35K ASP* 2.8 41.8 + - - -
39K LEU* 3.7 26.1 - - + +
44K GLY 3.0 24.7 + - - -
45K ASN* 2.8 19.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 135 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131H PHE 2.8 6.6 + - - -
132H GLU 3.2 11.8 + - - -
133H MET 3.8 0.2 + - - -
134H ARG* 1.3 78.5 - - - +
136H TRP* 1.3 61.5 + - - +
137H GLU 4.1 0.5 + - - -
7007H MRD 3.5 18.9 - - - +
----------------------------------------------------------
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