Contacts of the helix formed by residues 117 - 137 (chain B) in PDB entry 1N8T
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 VAL 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B LEU* 4.6 1.6 - - + -
101B ALA* 4.0 24.0 - - + -
110B ILE* 2.9 24.1 + - + +
112B VAL* 3.8 30.1 - - + +
115B LYS* 3.9 6.5 - - - +
116B ASP* 1.3 71.7 - - - +
118B MET* 1.3 73.9 + - - +
119B PRO* 3.4 0.7 - - - -
120B GLU* 3.1 22.1 + - + +
121B VAL* 3.1 10.9 + - + +
268B TRP* 3.7 34.9 - - + +
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Residues in contact with MET 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA* 3.3 40.2 - - - +
104B ASN* 3.4 26.9 - - + +
107B ASN* 3.4 37.2 - - + +
108B THR 3.5 19.3 - - - +
110B ILE* 4.2 4.9 - - - +
116B ASP* 3.0 20.6 + - - +
117B VAL* 1.3 80.6 - - - +
119B PRO* 1.3 69.2 - - + +
121B VAL* 2.8 28.8 + - + +
122B ASN* 2.9 20.2 + - - +
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Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP* 3.4 32.5 - - + +
117B VAL 3.5 0.7 - - - -
118B MET* 1.3 94.4 - - + +
120B GLU* 1.3 64.5 + - - +
122B ASN* 3.3 6.7 + - + +
123B LYS* 2.9 30.7 + - - +
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Residues in contact with GLU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ASP 5.2 2.7 - - - +
117B VAL* 3.1 16.6 + - + +
119B PRO* 1.3 81.0 - - - +
121B VAL* 1.3 68.9 + - - +
123B LYS* 3.3 20.0 + - - +
124B VAL* 3.2 26.5 + - - +
264B GLU* 5.4 3.6 - - - +
266B TRP* 3.7 25.6 + - + +
268B TRP* 6.0 0.9 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA 3.8 19.5 - - - +
102B LEU* 3.8 23.6 - - + +
117B VAL* 3.1 16.1 + - + +
118B MET* 2.8 17.1 + - + +
120B GLU* 1.3 78.0 - - - +
122B ASN* 1.3 68.8 + - - +
124B VAL* 3.3 3.8 + - - +
125B LEU* 3.1 39.2 + - + +
266B TRP* 3.8 11.9 - - + -
268B TRP* 3.9 25.8 - - + -
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Residues in contact with ASN 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ASN 5.6 0.2 + - - -
105B ARG* 5.1 6.1 - - - +
107B ASN* 2.8 36.3 + - - +
118B MET* 2.9 20.5 + - - +
119B PRO* 3.9 5.5 - - + +
121B VAL* 1.3 80.5 - - - +
123B LYS* 1.3 60.5 + - - +
125B LEU* 3.2 22.4 + - - +
126B ASP* 2.8 42.2 + - - +
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Residues in contact with LYS 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B PRO 2.9 18.4 + - - +
120B GLU* 3.7 23.5 + - - +
122B ASN* 1.3 75.6 - - - +
124B VAL* 1.3 62.3 + - + +
126B ASP* 3.4 7.6 + - - +
127B LYS* 2.9 38.2 + - + +
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Residues in contact with VAL 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B GLU* 3.2 13.1 + - - +
121B VAL 3.7 6.7 - - - +
122B ASN 3.2 0.6 - - - -
123B LYS* 1.3 78.4 - - + +
125B LEU* 1.3 61.9 + - + +
127B LYS* 3.0 10.2 + - + +
128B MET* 2.8 41.7 + - + +
263B PHE* 4.6 4.3 - - + -
264B GLU* 3.4 45.1 - - + +
266B TRP* 3.8 14.6 - - + -
278B ALA* 3.9 20.9 - - + +
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Residues in contact with LEU 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B LEU 4.0 10.8 - - - +
105B ARG* 4.4 10.8 - - - +
121B VAL* 3.1 31.5 + - + +
122B ASN* 3.7 24.7 - - - +
124B VAL* 1.3 76.9 - - + +
126B ASP* 1.3 64.8 + - - +
128B MET* 3.1 11.9 + - - -
129B LYS* 2.9 21.5 + - - +
276B TRP 4.7 6.1 - - - +
277B SER* 5.9 0.7 - - - -
289B PHE* 3.3 24.2 - - + -
292B PHE* 3.8 19.7 - - + -
296B LEU* 3.7 26.9 - - + -
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Residues in contact with ASP 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASN* 2.8 31.0 + - - +
123B LYS* 3.7 7.6 - - - +
125B LEU* 1.3 73.9 - - - +
127B LYS* 1.3 63.4 + - - +
129B LYS* 3.4 11.9 + - - +
130B ALA* 3.1 23.0 + - - +
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Residues in contact with LYS 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B LYS* 2.9 24.7 + - + +
124B VAL* 3.2 13.5 - - + +
126B ASP* 1.3 78.8 - - - +
128B MET* 1.3 61.9 + - - +
130B ALA* 3.3 7.2 + - + +
131B PHE* 3.1 23.1 + - + +
259B PRO 4.6 2.2 + - - -
260B GLN* 3.1 42.2 + - - +
262B MET 3.5 21.9 + - - +
263B PHE* 3.9 17.9 - - + -
264B GLU* 6.2 0.6 - - - +
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Residues in contact with MET 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B VAL* 2.8 30.7 + - + +
125B LEU* 3.5 22.0 - - - +
127B LYS* 1.3 71.1 - - - +
129B LYS* 1.3 58.2 + - - +
131B PHE* 3.4 2.1 + - - +
132B CYS* 2.8 32.1 + - - +
263B PHE* 3.8 24.9 - - + -
277B SER 3.5 21.1 - - - +
278B ALA* 3.6 21.5 - - - -
281B LEU* 3.5 38.9 - - + +
284B ALA* 5.0 0.7 - - + -
289B PHE* 3.7 9.6 - - + -
292B PHE* 3.9 18.8 - - + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B LEU 2.9 12.1 + - - +
126B ASP* 3.5 15.9 - - - +
128B MET* 1.3 74.6 - - - +
130B ALA* 1.3 56.9 + - - +
132B CYS* 3.1 4.0 + - - +
133B GLN* 2.7 41.1 + - + +
289B PHE* 3.6 46.0 - - + +
290B ASP* 4.3 15.8 + - - -
293B GLU* 5.2 7.5 + - - +
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Residues in contact with ALA 130 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ASP 3.1 10.8 + - - +
127B LYS* 3.3 9.8 + - + +
129B LYS* 1.3 80.0 - - - +
131B PHE* 1.3 61.9 + - - +
133B GLN* 3.4 8.1 - - - +
134B ARG* 3.1 29.3 + - + +
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Residues in contact with PHE 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B LYS* 3.1 15.7 + - + +
128B MET 3.8 2.0 - - - +
130B ALA* 1.3 73.1 - - - +
132B CYS* 1.3 70.0 + - - +
134B ARG* 2.9 10.9 + - - +
135B VAL* 2.9 41.2 + - + +
140B TRP* 3.6 40.4 - + - -
204B LEU* 3.6 29.6 - - + -
243B VAL* 3.6 22.2 - - + -
261B ASN* 4.5 6.1 - - - -
263B PHE* 3.6 24.7 - + + -
281B LEU* 3.9 29.2 - - + -
285B LEU* 4.2 5.6 - - + -
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Residues in contact with CYS 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B MET 2.8 22.9 + - - +
129B LYS* 3.5 4.9 - - - +
131B PHE* 1.3 73.5 - - - +
133B GLN* 1.3 63.4 + - - +
135B VAL* 4.0 0.2 - - - +
136B ARG* 3.0 42.2 + - - +
281B LEU* 4.9 2.0 - - + -
284B ALA* 3.6 31.0 - - + -
285B LEU* 3.8 21.5 - - + -
289B PHE* 4.3 22.2 - - + -
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Residues in contact with GLN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B LYS* 2.7 22.1 + - + +
130B ALA* 3.4 13.2 - - - +
132B CYS* 1.3 72.6 - - - +
134B ARG* 1.3 66.2 + - + +
136B ARG* 5.0 4.9 - - - +
137B SER* 3.1 40.5 + - - -
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Residues in contact with ARG 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ALA* 3.1 17.9 - - - +
131B PHE* 2.9 9.9 + - - +
133B GLN* 1.3 76.9 - - + +
135B VAL* 1.3 59.8 + - - +
139B ASP* 3.1 46.7 + - - +
140B TRP* 2.8 68.7 + - + +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 2.9 52.8 + - + +
134B ARG* 1.3 75.3 - - - +
136B ARG* 1.3 66.7 + - - +
138B GLY* 3.3 11.3 + - - -
140B TRP* 3.9 18.9 - - + +
148B ILE* 3.9 44.3 + - + +
151B VAL* 4.8 3.1 - - + -
178B PRO* 5.1 5.2 - - + -
204B LEU* 4.3 7.0 - - + -
285B LEU* 3.6 21.1 - - + -
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Residues in contact with ARG 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132B CYS* 3.0 37.1 + - - +
133B GLN* 4.5 5.8 - - - +
135B VAL* 1.3 77.7 - - - +
137B SER* 1.3 61.6 + - - +
138B GLY* 3.0 1.8 + - - -
173B TYR 4.8 0.2 + - - -
174B SER 4.2 0.6 + - - -
175B SER 3.6 15.0 + - - -
176B GLY* 3.9 20.8 + - - +
177B GLY* 3.2 20.4 - - - +
178B PRO* 4.6 8.7 - - + -
285B LEU* 2.9 24.9 + - + +
286B HIS 3.1 26.3 + - - -
287B VAL* 3.5 4.4 - - - +
288B GLY* 3.5 24.9 - - - +
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Residues in contact with SER 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B GLN* 3.1 38.6 + - - -
136B ARG* 1.3 79.0 - - - +
138B GLY* 1.3 57.8 + - - +
139B ASP* 3.2 22.2 + - - +
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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) + - + + + + + -
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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