Contacts of the helix formed by residues 3 - 15 (chain B) 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 ASP 3 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1B GLN 4.7 2.9 - - - +
2B GLY* 1.3 74.6 - - - +
4B ILE* 1.3 61.8 + - - +
5B GLY* 3.0 7.9 + - - +
6B ILE* 3.1 36.6 + - + +
7B ASP* 4.3 1.7 + - - +
156B LYS* 2.9 32.4 + - - +
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Residues in contact with ILE 4 (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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102A ASN* 4.2 21.3 - - - +
150A GLU 4.0 6.7 - - - +
151A TYR* 3.6 39.5 - - + +
154A LYS* 4.5 10.3 - - - +
160A GLY 5.9 0.9 - - - +
2B GLY 3.7 5.6 + - - +
3B ASP* 1.3 72.4 - - - +
5B GLY* 1.3 57.0 + - - +
6B ILE 3.3 0.2 + - - -
7B ASP* 3.5 9.2 + - + +
8B ASN* 3.0 40.3 + - - +
186B ASP 3.4 24.7 - - - +
187B GLY 3.8 9.0 - - - +
188B LEU* 4.0 5.6 - - + -
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Residues in contact with GLY 5 (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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3B ASP* 3.0 4.2 - - - +
4B ILE* 1.3 82.5 - - - +
6B ILE* 1.3 55.6 + - - +
9B LEU* 2.9 35.9 + - - +
183B THR* 3.8 19.2 - - - +
187B GLY* 3.5 27.8 - - - -
192B PHE* 5.3 0.4 - - - -
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Residues in contact with ILE 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ASP* 3.1 30.5 + - + +
5B GLY* 1.3 75.6 - - - +
7B ASP* 1.3 71.5 + - - +
9B LEU* 4.0 2.1 - - - +
10B ARG* 3.2 41.0 + - - +
156B LYS* 3.5 55.4 - - + +
157B PHE* 3.6 33.2 - - + -
183B THR* 5.9 0.7 - - + -
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Residues in contact with ASP 7 (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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102A ASN* 5.4 10.6 + - - +
154A LYS* 5.6 3.4 - - - +
3B ASP 4.3 1.1 + - - -
4B ILE* 3.5 11.6 + - + +
6B ILE* 1.3 82.8 - - - +
8B ASN* 1.3 60.4 + - - +
10B ARG* 2.9 26.8 + - - +
11B ASN* 2.8 32.9 + - - +
15B LYS* 4.8 0.9 + - - -
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Residues in contact with ASN 8 (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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154A LYS* 2.8 29.3 + - - +
4B ILE* 3.0 32.4 + - - +
5B GLY 4.1 0.9 - - - +
7B ASP* 1.3 73.6 - - - +
9B LEU* 1.3 60.7 + - - +
11B ASN* 4.5 2.5 + - - +
12B PHE* 2.8 52.5 + - + +
187B GLY 2.9 26.4 + - - +
188B LEU* 3.8 8.5 - - - +
189B PRO* 3.8 12.3 - - - +
192B PHE* 3.7 13.5 - - + -
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Residues in contact with LEU 9 (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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5B GLY 2.9 21.5 + - - +
6B ILE 4.0 2.5 - - - +
8B ASN* 1.3 71.0 - - - +
10B ARG* 1.3 65.5 + - - +
13B TYR* 3.0 57.5 + - + +
130B ARG* 4.7 2.5 - - - +
140B TYR* 4.1 24.4 - - + +
157B PHE* 4.0 21.5 - - + -
180B LEU 4.2 1.8 - - - +
181B PHE 4.1 9.4 - - - -
182B TYR 3.6 20.4 - - - +
183B THR* 3.7 24.0 - - + -
192B PHE* 3.9 17.3 - - + -
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Residues in contact with ARG 10 (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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6B ILE* 3.2 27.2 + - - +
7B ASP* 2.9 34.8 + - - +
9B LEU* 1.3 79.1 - - - +
11B ASN* 1.3 63.4 + - - +
14B THR* 2.6 38.2 + - - +
15B LYS* 3.5 19.8 + - + +
134B GLN* 3.9 11.7 - - - +
140B TYR* 2.9 41.1 + - + -
141B GLY 2.9 14.0 + - - -
142B HIS* 3.7 27.7 - - - +
157B PHE 3.2 15.8 + - - -
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Residues in contact with ASN 11 (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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154A LYS* 5.4 0.6 - - - +
215A TYR* 4.1 23.7 + - - -
217A ALA* 4.4 16.1 - - - +
7B ASP 2.8 21.7 + - - +
8B ASN* 4.0 3.9 + - - +
10B ARG* 1.3 75.0 - - - +
12B PHE* 1.3 86.0 + - + +
15B LYS* 3.0 39.0 + - - +
16B LYS* 2.9 40.0 + - - +
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Residues in contact with PHE 12 (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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154A LYS* 4.4 23.8 - - + -
8B ASN* 2.8 53.6 + - + +
11B ASN* 1.3 92.5 - - - +
13B TYR* 1.3 60.2 + - - +
16B LYS* 3.6 38.7 - - + +
18B PHE* 4.0 4.2 - - - -
67B ILE* 3.5 43.6 - - + +
68B SER 3.7 9.0 - - - -
69B TYR* 3.9 14.6 - - + -
70B ASN 5.9 0.2 - - - -
189B PRO* 3.6 26.0 - - + -
192B PHE* 4.3 15.5 - + + -
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Residues in contact with TYR 13 (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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9B LEU* 3.0 49.8 + - + +
12B PHE* 1.3 78.6 - - - +
14B THR* 1.3 69.7 + - + +
15B LYS 4.0 0.4 - - - -
16B LYS 5.3 0.4 - - - -
18B PHE* 3.2 26.7 - - - -
67B ILE* 3.7 22.2 - - + -
127B VAL* 3.9 13.5 - - + +
130B ARG* 3.5 51.1 + - + -
131B LYS* 3.8 6.6 - - - +
140B TYR* 4.1 8.1 - - + -
192B PHE* 4.1 18.1 + + - -
193B LEU* 4.2 2.7 - - + +
195B ILE* 4.3 4.2 - - - +
196B TYR* 2.7 38.3 + + - -
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Residues in contact with THR 14 (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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10B ARG* 2.6 29.7 + - - +
13B TYR* 1.3 93.0 - - + +
15B LYS* 1.3 68.0 + - - +
16B LYS 5.0 1.1 - - - -
130B ARG 4.1 7.2 - - - +
131B LYS* 4.1 26.0 - - - +
134B GLN* 3.6 41.8 + - + +
140B TYR* 3.8 14.6 - - + -
7003B EDO 4.5 12.3 + - - -
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Residues in contact with LYS 15 (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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217A ALA* 6.3 4.3 - - - +
7B ASP 4.8 1.0 + - - -
10B ARG* 3.7 22.5 - - + +
11B ASN* 3.0 44.9 + - - +
13B TYR 4.0 0.2 - - - -
14B THR* 1.3 87.2 + - - +
16B LYS* 1.3 68.8 + - - +
17B ASP* 3.4 9.0 + - - +
131B LYS* 6.1 0.8 - - - -
142B HIS 6.1 0.4 - - - +
7003B EDO 5.3 6.5 - - - +
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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
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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