Contacts of the helix formed by residues 159 - 175 (chain A) in PDB entry 1NVT
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 THR 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ASN* 3.2 10.1 + - - +
158A ARG* 1.3 87.7 - - + +
160A VAL* 1.3 65.5 + - - +
161A GLU* 3.2 8.7 - - - -
162A LYS* 3.0 30.4 + - - +
163A ALA 3.5 1.6 + - - -
288A NAP 2.8 24.9 + - - +
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Residues in contact with VAL 160 (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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157A ASN 4.2 3.4 - - - +
158A ARG 3.5 4.5 + - - +
159A THR* 1.3 68.7 - - - +
161A GLU* 1.3 81.7 + - + +
163A ALA* 2.6 31.6 + - + +
164A GLU* 2.7 15.8 + - + +
184A PHE* 4.9 11.8 - - + -
185A SER* 4.2 4.3 - - - +
186A GLY* 4.0 30.3 - - - +
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Residues in contact with GLU 161 (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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159A THR* 3.2 7.2 + - - -
160A VAL* 1.3 90.0 - - + +
162A LYS* 1.3 57.4 + - - +
164A GLU* 3.4 11.6 + - - +
165A ALA* 3.0 30.2 + - - +
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Residues in contact with LYS 162 (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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136A ALA* 3.9 36.1 - - + +
137A GLY* 4.6 3.8 - - - +
157A ASN* 3.9 3.6 - - - +
159A THR* 3.0 22.7 + - - +
160A VAL 3.0 0.8 - - - -
161A GLU* 1.3 75.5 - - - +
163A ALA* 1.3 66.4 + - - +
165A ALA* 3.5 5.6 + - - +
166A LEU* 3.1 23.4 + - - +
288A NAP 2.5 32.3 + - - -
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Residues in contact with ALA 163 (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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136A ALA* 4.5 1.2 - - - +
155A ILE* 3.4 36.4 - - + +
157A ASN* 3.9 20.4 - - + -
159A THR 3.5 0.8 + - - -
160A VAL* 2.6 17.8 + - - +
162A LYS* 1.3 72.1 - - - +
164A GLU* 1.3 65.5 + - - +
166A LEU* 3.2 3.1 + - - +
167A ALA* 3.0 23.9 + - - +
184A PHE* 3.7 8.5 - - + +
185A SER 4.0 8.3 - - - +
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Residues in contact with GLU 164 (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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160A VAL* 2.7 16.0 + - + +
161A GLU* 3.7 15.7 - - - +
163A ALA* 1.3 73.6 - - - +
165A ALA* 1.3 63.0 + - - +
167A ALA* 3.3 1.7 + - - +
168A LYS* 3.0 52.1 + - + +
178A PHE* 4.2 2.0 - - + -
184A PHE* 3.4 47.2 - - + +
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Residues in contact with ALA 165 (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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161A GLU 3.0 18.2 + - - +
162A LYS* 3.7 7.0 - - - +
164A GLU* 1.3 78.3 - - - +
166A LEU* 1.3 61.3 + - - +
168A LYS* 3.5 8.9 + - - +
169A GLU* 3.2 23.2 + - - +
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Residues in contact with LEU 166 (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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136A ALA* 4.2 21.8 - - + +
140A ALA* 4.5 4.0 - - + +
141A ARG* 3.6 58.1 - - + +
145A PHE* 4.2 2.9 - - + -
155A ILE* 3.4 32.5 - - + -
162A LYS 3.1 17.6 + - - +
163A ALA* 3.2 4.5 + - - +
165A ALA* 1.3 73.4 - - - +
167A ALA* 1.3 67.0 + - - +
169A GLU* 3.2 5.9 + - - +
170A ILE* 3.0 42.0 + - + +
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Residues in contact with ALA 167 (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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155A ILE* 3.8 6.2 - - + +
163A ALA 3.0 15.9 + - - +
164A GLU 3.7 1.8 - - - +
166A LEU* 1.3 76.5 - - - +
168A LYS* 1.3 57.0 + - - +
171A ALA* 3.0 26.9 + - - +
178A PHE* 3.7 17.0 - - + -
182A VAL* 3.1 32.4 - - + +
183A LYS 3.8 17.0 - - - +
184A PHE* 4.0 7.2 - - + -
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Residues in contact with LYS 168 (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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164A GLU* 3.0 42.4 + - + +
165A ALA* 3.8 8.3 - - - +
167A ALA* 1.3 73.6 - - - +
169A GLU* 1.3 61.7 + - - +
171A ALA* 4.0 0.9 - - - +
172A GLU* 2.9 32.6 + - - +
178A PHE* 3.2 31.4 - - + -
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Residues in contact with GLU 169 (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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141A ARG* 2.7 45.6 + - - -
145A PHE* 3.7 7.7 - - + -
165A ALA 3.2 12.1 + - - +
166A LEU* 3.6 10.2 - - - +
168A LYS* 1.3 79.0 - - - +
170A ILE* 1.3 57.1 + - - +
172A GLU* 3.8 4.9 - - - +
173A LYS* 3.0 65.1 + - + +
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Residues in contact with ILE 170 (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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144A ALA* 3.3 37.0 - - + +
145A PHE* 3.8 26.7 - - + +
148A ALA* 3.5 28.0 - - + -
153A ILE* 4.0 3.6 - - + -
155A ILE* 3.7 15.5 - - + -
166A LEU* 3.0 23.9 + - + +
167A ALA 3.8 3.8 - - - +
168A LYS 3.2 0.2 - - - -
169A GLU* 1.3 74.3 - - - +
171A ALA* 1.3 60.8 + - - +
174A LEU* 2.8 48.2 + - + +
182A VAL* 4.0 11.2 - - + -
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Residues in contact with ALA 171 (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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167A ALA 3.0 19.1 + - - +
168A LYS 4.0 2.7 - - - +
170A ILE* 1.3 75.7 - - - +
172A GLU* 1.3 54.0 + - - +
175A ASN* 2.7 15.6 + - - -
176A LYS* 2.7 46.8 + - - +
178A PHE* 4.1 19.5 - - + -
182A VAL* 4.0 20.6 - - + +
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Residues in contact with GLU 172 (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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168A LYS 2.9 20.2 + - - +
169A GLU* 3.8 5.9 - - - +
171A ALA* 1.3 76.1 - - - +
173A LYS* 1.3 79.0 + - - +
175A ASN* 2.9 22.2 + - - +
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Residues in contact with LYS 173 (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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90A GLN 4.0 9.1 + - - -
91A LEU* 3.1 40.3 + - + +
93A GLY* 5.4 1.2 - - - +
141A ARG* 4.6 1.4 - - - +
145A PHE* 3.9 25.4 - - + -
169A GLU* 3.0 41.6 + - + +
172A GLU* 1.3 97.0 + - - +
174A LEU* 1.3 63.4 + - + +
175A ASN* 5.0 0.9 - - - +
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Residues in contact with LEU 174 (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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91A LEU* 3.8 29.4 - - + -
145A PHE* 3.5 32.8 - - + +
148A ALA* 3.8 12.8 - - + -
149A LYS* 4.0 20.9 - - + +
170A ILE* 2.8 40.5 + - + +
173A LYS* 1.3 75.3 - - - +
175A ASN* 1.3 72.5 + - - +
176A LYS* 3.0 22.5 + - + +
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Residues in contact with ASN 175 (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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171A ALA 2.7 11.7 + - - -
172A GLU 2.9 9.8 + - - +
173A LYS 5.0 0.7 - - - +
174A LEU* 1.3 83.7 - - - +
176A LYS* 1.3 64.0 + - - +
181A GLU* 4.8 0.2 - - - +
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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
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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