Contacts of the helix formed by residues 120 - 135 (chain A) in PDB entry 1N54
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 ASN 120 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A SER* 2.9 19.0 + - - +
118A ALA* 3.2 29.5 + - - +
119A ASN* 1.3 78.9 + - - +
121A TYR* 1.3 58.4 + - - +
122A ASN* 3.2 4.9 - - - +
123A GLU* 3.0 31.4 + - + +
124A ALA* 2.9 26.9 + - - +
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Residues in contact with TYR 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A LEU* 3.3 39.9 + - + +
119A ASN* 3.2 28.7 + - - -
120A ASN* 1.3 75.0 - - - +
122A ASN* 1.3 63.7 + - - +
124A ALA* 4.0 4.0 - - - -
125A VAL* 3.2 28.6 + - - +
165A ARG* 5.4 1.4 + - - -
168A TRP* 3.2 42.0 + + - +
169A TYR* 5.0 8.1 + + - -
274A PRO* 5.7 2.6 + - - +
280A SER* 4.7 3.8 + - - -
281A VAL 3.3 29.2 - - - -
282A TYR* 3.9 24.9 - + - -
283A PRO* 3.6 27.3 - - + +
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Residues in contact with ASN 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119A ASN 5.7 1.0 + - - -
120A ASN* 3.2 2.6 + - - +
121A TYR* 1.3 79.2 - - - +
123A GLU* 1.3 61.0 + - - +
125A VAL* 3.9 9.6 + - - +
126A TYR* 3.1 31.9 - - + +
168A TRP* 5.3 0.2 - - - +
283A PRO* 4.2 22.9 - - - +
286A ARG* 5.0 7.3 + - - -
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Residues in contact with GLU 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A ARG* 2.9 54.7 + - + -
78A LEU* 3.6 10.4 - - + +
111A GLN* 5.3 1.6 + - - -
115A SER* 4.2 13.7 + - - +
120A ASN* 3.0 34.8 + - + +
122A ASN* 1.3 79.5 - - - +
124A ALA* 1.3 56.5 + - - +
125A VAL 3.2 0.2 - - - -
126A TYR* 2.7 46.1 + - + +
127A LEU* 3.6 5.9 + - + +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 3.7 13.7 - - + +
115A SER* 4.2 7.3 - - - -
116A LEU* 3.6 31.2 - - + -
120A ASN 2.9 15.1 + - - +
121A TYR* 3.5 6.7 + - - +
123A GLU* 1.3 71.9 - - - +
125A VAL* 1.3 65.1 + - - +
126A TYR 3.0 2.0 - - - -
127A LEU* 3.1 19.3 + - - +
128A VAL* 3.3 16.5 + - - +
168A TRP* 3.8 7.9 - - + -
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Residues in contact with VAL 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A TYR 3.2 6.9 + - - +
122A ASN* 4.0 8.7 - - - +
123A GLU 3.2 0.4 - - - -
124A ALA* 1.3 77.9 - - - +
126A TYR* 1.3 64.6 + - + +
128A VAL* 3.8 7.3 - - - +
129A ARG* 2.9 55.0 + - - +
168A TRP* 2.8 42.4 - - + +
171A TYR* 4.2 14.1 - - + -
172A ALA* 4.2 11.2 - - + +
175A SER* 4.2 9.9 - - - +
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A ALA 4.0 10.4 - - - +
77A ARG* 3.7 25.4 - - - +
80A PRO* 3.7 32.8 - - + -
83A LEU* 4.5 3.6 - - - +
122A ASN* 3.1 24.8 + - + +
123A GLU* 2.7 31.6 + - + +
125A VAL* 1.3 81.1 - - + +
127A LEU* 1.3 62.3 + - - +
129A ARG* 3.3 16.2 + - - +
130A PHE* 3.0 20.8 + - - +
316A GLU* 4.2 18.2 + - - -
320A CYS* 4.1 10.2 - - - -
323A LYS* 3.7 26.8 - - + +
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Residues in contact with LEU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A CYS 5.1 0.9 - - - +
76A ALA* 4.5 1.1 - - + +
77A ARG* 4.0 31.4 - - + +
108A MET* 4.1 25.8 - - + +
111A GLN* 4.0 17.0 - - + -
112A LEU* 3.3 55.9 - - + +
115A SER* 4.1 7.6 - - - +
123A GLU* 4.2 7.4 - - + +
124A ALA* 3.4 8.3 - - - +
126A TYR* 1.3 73.1 - - - +
128A VAL* 1.3 58.9 + - - +
130A PHE* 2.5 30.3 + - - +
131A LEU* 2.8 18.1 + - + +
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Residues in contact with VAL 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A LEU* 4.0 16.8 - - + +
124A ALA 3.3 11.4 + - - +
125A VAL* 3.8 9.4 - - - +
127A LEU* 1.3 78.1 - - - +
129A ARG* 1.3 62.5 + - - +
131A LEU* 4.0 9.3 - - - +
132A SER* 3.1 27.7 + - - -
145A MET* 4.9 7.2 - - + +
148A MET* 5.7 0.4 - - - -
149A PHE* 3.9 19.1 - - + -
152A PHE* 3.8 27.4 - - + -
168A TRP* 5.2 1.8 - - + -
172A ALA* 3.4 20.6 - - + +
176A SER* 3.3 18.6 - - - +
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Residues in contact with ARG 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A LEU* 4.2 13.9 - - + +
125A VAL* 2.9 46.4 + - - +
126A TYR* 3.5 14.8 - - - +
128A VAL* 1.3 78.4 - - - +
130A PHE* 1.3 61.0 + - - +
132A SER* 3.6 3.1 - - - -
133A ASP* 3.3 21.1 + - - +
171A TYR* 4.1 9.7 + - - -
175A SER* 3.6 23.9 + - - -
176A SER* 3.9 14.8 + - - +
179A TRP* 2.9 49.5 - - + +
312A PHE* 4.0 5.7 - - - -
316A GLU* 3.3 38.9 + - - +
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Residues in contact with PHE 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LEU 5.1 1.6 - - - -
75A VAL 5.1 1.1 - - - -
76A ALA* 3.9 27.6 - - + +
83A LEU* 3.5 29.4 - - + +
86A TYR* 3.7 16.6 - - + -
87A THR* 3.3 43.1 - - + +
90A VAL* 4.2 4.3 - - + -
104A PHE* 3.8 27.4 - + - -
108A MET* 3.5 22.4 - - + -
126A TYR 3.0 11.4 + - - +
127A LEU* 2.5 16.2 + - - +
129A ARG* 1.3 68.0 - - - +
131A LEU* 1.3 69.0 + - - +
132A SER 3.1 0.7 - - - -
133A ASP* 2.8 15.9 + - - +
134A LEU* 3.0 20.9 + - + +
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Residues in contact with LEU 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A VAL* 5.1 3.1 - - + -
108A MET* 3.8 40.2 - - + -
109A ILE* 3.4 29.8 - - + -
112A LEU* 4.4 17.0 - - + -
127A LEU* 2.8 20.4 + - + +
128A VAL* 4.0 5.6 - - + +
130A PHE* 1.3 72.6 - - - +
132A SER* 1.3 63.2 + - - +
134A LEU* 2.9 37.4 + - + +
135A VAL* 3.6 4.2 + - - +
140A ILE* 3.8 19.2 - - + +
145A MET* 4.3 22.9 - - + -
148A MET* 5.1 2.2 - - + -
268A LEU* 5.2 1.3 - - + -
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Residues in contact with SER 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A VAL 3.1 20.3 + - - -
129A ARG 3.6 5.8 - - - -
131A LEU* 1.3 78.0 - - - +
133A ASP* 1.3 65.9 + - - +
135A VAL* 2.9 23.4 + - - +
136A ASN 4.2 0.2 + - - -
145A MET* 4.3 11.8 - - - +
149A PHE* 3.4 17.8 - - - -
176A SER* 3.3 20.4 - - - -
179A TRP* 5.6 0.4 - - - -
180A VAL* 3.2 30.7 - - - +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83A LEU* 4.9 4.5 - - + -
84A THR* 3.7 14.1 - - - +
87A THR* 2.6 35.5 + - + +
129A ARG 3.3 10.3 + - - +
130A PHE 2.8 13.5 + - - +
132A SER* 1.3 75.3 - - - +
134A LEU* 1.3 54.0 + - - +
136A ASN* 2.8 31.5 + - - +
137A CYS* 3.1 10.5 + - - -
179A TRP* 4.0 11.6 - - + +
180A VAL* 4.3 3.1 - - - +
251A ARG* 2.9 15.8 + - - -
253A TYR* 2.5 30.4 + - - -
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87A THR* 3.9 29.2 - - - +
90A VAL* 4.3 12.6 - - + -
104A PHE* 4.4 10.3 - - + -
105A VAL* 4.8 4.3 - - + -
130A PHE* 3.0 22.9 + - + +
131A LEU* 2.9 31.7 + - + +
133A ASP* 1.3 75.5 - - - +
135A VAL* 1.3 55.2 + - - +
136A ASN 3.2 0.2 - - - -
137A CYS* 3.0 20.7 + - - +
139A VAL* 3.3 46.7 + - + -
140A ILE* 3.7 29.6 - - + -
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Residues in contact with VAL 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A LEU 4.0 7.2 - - - +
132A SER 2.9 18.4 + - - +
133A ASP 2.8 0.2 + - - -
134A LEU* 1.3 79.3 - - - +
136A ASN* 1.3 65.8 + - - +
137A CYS 3.0 1.2 + - - -
138A HIS* 3.6 9.7 + - - -
140A ILE* 3.7 27.2 - - + +
141A ALA 4.7 0.9 - - - +
142A ALA* 3.7 29.6 - - + +
145A MET* 4.0 26.5 - - + -
180A VAL* 3.8 10.8 - - + -
183A GLU* 3.8 14.3 - - - +
184A LEU* 4.7 5.4 - - + -
265A GLN* 5.6 0.9 - - - +
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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
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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