Contacts of the helix formed by residues 122 - 138 (chain A) in PDB entry 2NTT
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 ALA 122 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A VAL 3.5 2.4 + - - -
121A THR* 1.3 71.6 - - - +
123A GLN* 1.3 57.8 + - - +
125A ILE 3.3 1.4 + - - -
126A ASP* 2.8 32.2 + - - +
168A PHE* 3.4 21.2 - - + -
176A PHE* 3.7 25.8 - - + -
178A TYR* 3.5 25.4 - - + +
200A LYS* 2.9 18.4 + - + +
201A THR* 4.3 0.4 - - - +
202A VAL* 4.9 3.1 - - + +
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Residues in contact with GLN 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE 3.9 0.7 - - - -
66A GLY* 3.3 11.6 - - - -
67A ILE* 3.0 37.2 + - - +
78A ILE* 4.1 2.9 - - - +
79A TYR 2.7 28.0 + - - +
81A GLY* 3.5 12.2 + - - +
121A THR* 3.0 11.7 - - - +
122A ALA* 1.3 77.6 - - - +
124A GLU* 1.3 65.0 + - - +
126A ASP* 3.2 1.0 + - - -
127A VAL* 2.9 33.5 + - + +
193A LEU* 5.3 0.8 - - - +
196A TYR* 3.5 55.5 - - + +
200A LYS 4.7 0.4 + - - -
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Residues in contact with GLU 124 (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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65A PHE* 3.4 39.6 - - + +
114A SER 4.1 0.5 - - - +
115A THR* 4.0 10.2 + - - -
117A LYS* 2.9 36.1 + - - +
120A VAL* 3.6 15.6 - - + +
121A THR* 3.0 23.4 + - - +
123A GLN* 1.3 76.3 - - - +
125A ILE* 1.3 63.1 + - + +
127A VAL* 3.5 1.2 - - - +
128A LYS* 2.7 57.8 + - + +
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Residues in contact with ILE 125 (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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95A ILE* 4.0 19.7 - - + -
113A VAL* 4.2 9.7 - - + +
114A SER 4.5 7.6 - - - +
115A THR* 4.3 11.4 - - + -
120A VAL* 3.8 38.1 - - + -
121A THR 3.4 4.7 + - - +
122A ALA 3.3 5.5 + - - +
123A GLN 3.3 0.6 - - - -
124A GLU* 1.3 78.6 - - + +
126A ASP* 1.3 58.4 + - - +
128A LYS* 3.4 5.0 + - + +
129A LEU* 2.9 27.5 + - - +
168A PHE* 3.8 19.1 - - + -
207A PHE* 4.0 12.6 - - + -
209A LEU* 3.6 30.3 - - + -
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Residues in contact with ASP 126 (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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122A ALA 2.8 21.4 + - - +
123A GLN 3.7 3.1 - - - +
125A ILE* 1.3 74.4 - - - +
127A VAL* 1.3 57.1 + - - +
129A LEU* 3.1 8.0 + - - +
130A ARG* 2.9 65.1 + - - +
166A VAL* 3.5 15.8 - - - +
168A PHE* 4.2 6.5 - - + -
178A TYR* 3.4 22.8 - - + -
196A TYR* 2.5 27.8 + - + +
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Residues in contact with VAL 127 (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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13A TYR* 3.8 16.2 - - + +
18A PHE* 3.3 36.2 - - + -
65A PHE* 3.7 24.2 - - + -
66A GLY* 4.5 2.5 - - - -
67A ILE* 3.5 28.3 - - + -
123A GLN* 2.9 33.4 + - + +
124A GLU* 3.5 12.1 - - - +
126A ASP* 1.3 72.1 - - - +
128A LYS* 1.3 66.6 + - - +
130A ARG* 3.4 1.6 + - - +
131A LYS 3.1 18.7 + - - -
196A TYR* 3.9 7.9 - - + +
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Residues in contact with LYS 128 (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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18A PHE* 4.3 10.3 - - + -
65A PHE* 3.5 30.4 - - + -
112A LYS 3.6 21.6 - - - +
113A VAL* 4.0 8.1 - - + +
114A SER* 2.8 33.4 + - - +
115A THR* 4.8 1.2 - - - +
124A GLU* 2.7 49.3 + - + +
125A ILE* 3.7 5.8 - - + +
127A VAL* 1.3 78.7 - - + +
129A LEU* 1.3 63.1 + - - +
131A LYS* 3.4 3.5 + - - +
132A TYR* 3.0 22.9 + - - +
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Residues in contact with LEU 129 (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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97A ILE* 4.0 27.6 - - + -
113A VAL* 3.8 14.3 - - + +
125A ILE 2.9 19.2 + - - +
126A ASP* 3.1 9.4 + - - +
128A LYS* 1.3 76.7 - - - +
130A ARG* 1.3 56.9 + - - +
132A TYR* 3.1 6.8 + - + +
133A LEU* 2.8 50.7 + - + +
166A VAL* 3.4 38.4 - - + -
180A LEU* 4.9 2.5 - - + -
209A LEU* 4.5 7.9 - - + -
211A VAL* 3.6 22.9 - - + -
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Residues in contact with ARG 130 (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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9A LEU* 4.6 4.6 - - - +
13A TYR* 3.5 52.5 + - + -
14A THR* 4.2 4.0 - - - +
126A ASP* 2.9 54.4 + - - +
127A VAL 4.1 0.2 - - - +
129A LEU* 1.3 76.2 - - + +
131A LYS* 1.3 58.0 + - - +
133A LEU* 3.3 9.5 + - + +
134A GLN* 2.9 29.8 + - - +
139A ILE* 4.4 4.2 - - + +
140A TYR* 3.3 29.5 + - + +
178A TYR* 3.8 14.6 - - - +
179A ASP 3.7 17.9 + - - -
180A LEU* 3.5 34.2 + - + +
182A TYR* 5.2 2.0 + - - +
195A ILE* 4.1 6.5 - - - +
196A TYR* 3.9 0.6 + - - -
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Residues in contact with LYS 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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13A TYR 3.8 15.8 + - - +
14A THR* 4.2 26.3 + - - +
15A LYS 6.1 0.7 - - - -
16A LYS 6.1 1.1 - - - -
18A PHE* 3.8 23.6 - - + -
127A VAL 3.1 17.0 + - - +
128A LYS* 3.7 4.9 - - - +
129A LEU 3.3 0.2 - - - -
130A ARG* 1.3 75.1 - - - +
132A TYR* 1.3 62.9 + - - +
134A GLN* 3.3 4.0 + - - +
135A GLU* 2.6 56.2 + - + +
7010A EDO 5.5 2.9 - - - -
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Residues in contact with TYR 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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97A ILE* 5.1 2.0 - - + -
99A ILE* 6.3 0.2 - - + -
108A ILE* 3.5 35.6 - - + +
110A THR* 3.9 29.4 - - + +
112A LYS* 3.9 31.2 - - + -
113A VAL* 4.0 13.0 - - + -
128A LYS 3.0 14.5 + - - +
129A LEU* 3.4 11.2 - - + +
131A LYS* 1.3 76.6 - - - +
133A LEU* 1.3 68.3 + - + +
135A GLU* 3.1 9.6 + - - +
136A GLU* 2.9 64.6 + - + +
137A TYR* 4.8 12.2 + + - -
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Residues in contact with LEU 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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97A ILE* 6.3 0.4 - - + -
99A ILE* 3.8 28.7 - - + -
129A LEU* 2.8 45.6 + - + +
130A ARG* 3.3 8.5 + - - +
132A TYR* 1.3 79.0 - - + +
134A GLN* 1.3 58.1 + - - +
137A TYR* 2.8 44.8 + - + +
138A ASN 3.3 4.0 + - - -
139A ILE* 3.8 23.5 + - + -
180A LEU* 3.9 22.0 - - + -
211A VAL* 3.9 19.7 - - + -
213A ILE* 4.7 4.9 - - + -
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Residues in contact with GLN 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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10A ARG* 4.0 14.8 - - - +
14A THR* 3.6 21.6 + - + -
130A ARG 2.9 13.6 + - - +
131A LYS 3.5 8.3 - - - +
132A TYR 3.2 0.2 - - - -
133A LEU* 1.3 75.0 - - - +
135A GLU* 1.3 65.9 + - - +
138A ASN* 3.0 20.1 + - - -
139A ILE* 3.2 10.7 + - + +
140A TYR* 2.8 32.3 + - - -
141A GLY 2.8 26.9 + - - +
142A HIS 4.1 0.6 + - - -
143A ASN* 3.0 28.5 + - - +
7010A EDO 3.7 19.0 + - - +
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Residues in contact with GLU 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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112A LYS* 3.4 38.3 + - - +
131A LYS* 2.6 54.6 + - + +
132A TYR* 3.1 11.7 + - - +
134A GLN* 1.3 77.7 - - - +
136A GLU* 1.3 68.1 + - - +
143A ASN* 3.5 4.5 + - - -
145A THR* 4.4 1.9 + - - -
147A LYS* 3.2 24.6 - - - +
7010A EDO 3.4 29.2 + - - +
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Residues in contact with GLU 136 (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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112A LYS* 4.6 9.2 + - - -
132A TYR* 2.9 53.4 + - + +
135A GLU* 1.3 87.0 - - + +
137A TYR* 1.3 88.5 + - + +
138A ASN 3.7 0.2 - - - -
147A LYS* 2.8 48.7 + - - +
148A GLY* 3.6 15.9 + - - -
151A TYR* 4.8 0.7 - - - -
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Residues in contact with TYR 137 (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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99A ILE* 3.8 19.3 - - + +
101A ILE* 3.6 21.6 - - + +
106A LYS* 3.0 35.1 + - - -
108A ILE* 5.5 2.8 - - + +
132A TYR* 4.8 10.2 + + - -
133A LEU* 2.8 34.5 + - + +
136A GLU* 1.3 94.2 - - + +
138A ASN* 1.3 72.5 + - - +
139A ILE* 3.2 12.9 + - + -
148A GLY* 4.0 6.6 - - - +
151A TYR* 3.5 39.7 - + - +
160A GLY 5.5 0.7 + - - -
161A PHE* 3.7 16.6 - - + -
213A ILE* 4.1 9.4 - - + -
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Residues in contact with ASN 138 (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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133A LEU 3.3 0.4 + - - -
134A GLN* 3.0 19.4 + - - -
136A GLU 3.7 0.6 - - - -
137A TYR* 1.3 78.4 - - - +
139A ILE* 1.3 64.5 + - - +
140A TYR 3.2 3.1 - - - -
141A GLY* 2.9 29.7 + - - -
142A HIS* 3.9 4.0 - - - +
143A ASN* 2.9 47.3 + - - +
147A LYS 3.7 7.4 - - - +
148A GLY* 4.3 12.3 + - - +
149A GLU* 5.8 0.2 - - - +
152A GLY 5.0 1.0 + - - -
153A HIS* 4.1 15.4 + - - -
158A TYR 4.0 9.9 + - - -
159A SER* 3.0 12.8 - - - +
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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