Contacts of the helix formed by residues 126 - 138 (chain A) in PDB entry 3NIA
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 126 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99A TRP 3.8 4.5 - - - -
100A SER* 3.2 12.3 - - - -
101A PRO* 4.2 5.8 - - + -
102A ALA* 2.7 33.2 + - - +
103A THR* 2.7 30.3 + - - -
120A ALA* 3.2 24.4 + - + +
121A ALA* 4.0 1.6 - - - +
124A LEU* 3.1 6.6 - - + -
125A SER* 1.3 73.4 - - - +
127A ASN* 1.3 57.2 + - - +
128A GLY 3.1 6.4 + - - -
129A ALA* 2.9 20.5 + - + +
130A THR* 2.8 28.5 + - - -
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Residues in contact with ASN 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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67A LYS* 2.8 25.4 + - - -
97A VAL* 3.5 20.0 - - + -
98A GLU 2.9 20.4 + - - +
99A TRP* 2.9 25.3 + - - +
125A SER 3.7 3.6 + - - -
126A ASP* 1.3 69.9 - - - +
128A GLY* 1.3 66.2 + - - +
129A ALA 3.2 0.2 - - - -
130A THR* 3.2 5.6 + - - -
131A ASN* 3.0 27.4 + - - -
161A GLU* 3.1 27.0 - - + +
288A TBE 3.6 27.7 + - - +
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Residues in contact with GLY 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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95A MET* 3.7 23.9 - - - +
97A VAL* 3.5 3.1 - - - +
100A SER* 2.9 23.4 + - - -
103A THR* 3.5 11.9 - - - -
126A ASP* 3.1 2.6 + - - -
127A ASN* 1.3 75.4 - - - +
129A ALA* 1.3 56.0 + - - +
131A ASN* 3.3 4.4 + - - +
132A LEU* 2.9 28.1 + - - +
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Residues in contact with ALA 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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103A THR* 3.0 9.3 + - - +
112A MET* 4.6 3.6 - - - -
117A ALA* 3.6 30.6 - - + +
120A ALA* 4.1 7.2 - - + -
121A ALA* 4.3 0.9 - - - +
126A ASP* 2.9 28.5 + - + +
128A GLY* 1.3 72.6 - - - +
130A THR* 1.3 62.0 + - - +
132A LEU* 3.3 10.0 + - - +
133A LEU* 3.0 33.8 + - - +
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Residues in contact with THR 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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66A PHE* 3.5 37.5 - - + -
67A LYS* 3.2 22.1 - - + +
70A LEU* 4.0 10.2 - - + +
121A ALA* 3.6 11.3 - - - +
126A ASP 2.8 18.4 + - - -
127A ASN* 3.4 10.8 - - - -
129A ALA* 1.3 78.7 - - - +
131A ASN* 1.3 58.4 + - - +
133A LEU* 3.3 3.3 + - - +
134A LEU* 2.9 32.0 + - + +
161A GLU* 3.9 13.5 - - + +
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Residues in contact with ASN 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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95A MET* 4.0 15.3 + - - +
97A VAL* 4.1 16.0 - - - +
127A ASN 3.0 13.6 + - - +
128A GLY* 3.7 7.4 - - - +
130A THR* 1.3 76.0 - - - +
132A LEU* 1.3 63.1 + - - +
134A LEU* 3.3 8.0 + - - +
135A ARG* 2.9 24.6 + - - +
160A LYS* 3.4 30.2 - - + +
161A GLU* 3.0 52.7 + - - +
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Residues in contact with LEU 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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89A LEU* 3.8 36.2 - - + +
90A SER 4.1 0.7 - - - +
91A TYR* 3.8 39.3 - - + -
95A MET* 3.7 15.8 - - + -
103A THR* 5.6 0.7 - - + -
112A MET* 4.1 19.1 - - + -
117A ALA* 4.3 8.1 - - + -
128A GLY 2.9 17.5 + - - +
129A ALA* 3.4 7.2 - - - +
130A THR 3.2 0.2 - - - -
131A ASN* 1.3 78.5 - - - +
133A LEU* 1.3 60.6 + - - +
135A ARG* 3.5 29.9 + - - +
136A GLU* 3.2 20.1 + - - +
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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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70A LEU* 4.1 22.4 - - + -
71A ALA* 6.0 1.3 - - - -
74A VAL* 4.2 19.5 - - + -
89A LEU* 4.2 12.1 - - + -
114A VAL* 3.9 26.0 - - + +
117A ALA* 3.8 15.5 - - + +
118A ALA* 3.5 31.4 - - + +
121A ALA* 4.3 9.6 - - + -
129A ALA 3.0 17.8 + - - +
130A THR 3.6 4.5 - - - +
132A LEU* 1.3 73.5 - - - +
134A LEU* 1.3 65.9 + - - +
136A GLU* 3.0 8.0 + - + +
137A ILE* 2.9 28.4 + - + +
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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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66A PHE* 4.1 19.1 - - + -
70A LEU* 4.0 23.3 - - + -
130A THR* 2.9 21.6 + - + +
131A ASN* 3.3 11.0 + - - +
133A LEU* 1.3 76.7 - - - +
135A ARG* 1.3 62.7 + - - +
137A ILE* 3.3 5.1 + - + +
138A GLY 3.1 5.5 + - - -
139A GLY* 2.7 47.7 + - - +
140A PRO* 5.1 3.4 - - + -
143A MET* 4.6 2.7 - - + -
157A LEU* 3.9 25.6 - - + -
159A ARG 4.7 0.2 - - - +
160A LYS* 3.9 32.1 - - + -
161A GLU 5.0 0.2 - - - +
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Residues in contact with ARG 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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89A LEU* 5.9 0.4 - - - +
90A SER 3.0 27.7 + - - -
91A TYR* 4.3 3.0 - - - +
95A MET* 3.6 30.6 - - + +
131A ASN 2.9 18.0 + - - +
132A LEU* 3.7 12.9 + - - +
134A LEU* 1.3 76.1 - - - +
136A GLU* 1.3 64.2 + - - +
138A GLY* 3.7 7.6 + - - -
139A GLY* 4.9 1.6 - - - +
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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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77A ARG* 4.5 3.1 + - - -
83A GLU* 2.6 31.1 - - - +
87A ARG* 3.1 24.5 + - - -
89A LEU* 3.5 38.1 - - + +
114A VAL* 4.7 2.5 - - + -
132A LEU 3.2 9.9 + - - +
133A LEU* 3.0 11.5 + - + +
135A ARG* 1.3 83.2 - - - +
137A ILE* 1.3 64.8 + - + +
138A GLY 3.6 0.5 + - - -
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Residues in contact with ILE 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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70A LEU* 4.0 18.8 - - + -
73A LEU* 3.8 35.2 - - + -
74A VAL* 4.1 18.4 - - + -
77A ARG* 2.8 48.2 + - - +
83A GLU* 4.5 6.3 - - + +
114A VAL* 6.6 0.2 - - + -
133A LEU* 2.9 21.5 + - + +
134A LEU* 3.8 12.1 - - + +
136A GLU* 1.3 87.8 - - + +
138A GLY* 1.3 58.8 + - - +
139A GLY 3.9 11.7 - - - +
142A ALA* 3.2 17.6 - - + +
143A MET* 4.6 0.7 - - - +
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Residues in contact with GLY 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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134A LEU 3.1 2.0 + - - -
135A ARG 3.7 5.9 + - - -
136A GLU 3.4 3.6 + - - -
137A ILE* 1.3 78.6 - - - +
139A GLY* 1.3 65.9 + - - +
141A ALA* 4.3 6.8 + - - +
142A ALA* 3.7 13.7 + - - +
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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