Contacts of the helix formed by residues 127 - 140 (chain A) in PDB entry 4NZP
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 127 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLY* 1.3 73.3 - - - -
128A ASP* 1.3 64.4 + - - +
130A VAL* 3.2 17.3 + - - +
131A ARG* 3.4 37.3 + - + +
266A GLU* 4.7 0.6 + - - -
268A ARG* 3.4 34.1 - - - +
269A TYR* 2.8 30.8 + - + +
270A VAL* 3.1 15.7 + - - +
318A TYR* 2.9 36.7 + - - +
319A ASN 5.4 0.2 - - - +
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Residues in contact with ASP 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A THR* 3.8 4.0 - - - +
99A ARG* 2.9 41.5 + - - -
122A ALA* 3.8 16.8 - - + -
123A THR* 5.2 5.6 - - - +
126A GLY* 3.2 2.0 - - - -
127A ASN* 1.3 77.1 - - - +
129A GLN* 1.3 66.2 + - - +
131A ARG* 2.9 30.6 + - - +
132A PHE* 3.0 33.2 + - + -
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Residues in contact with GLN 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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120A HIS* 3.9 20.0 - - + -
122A ALA* 3.8 2.8 - - + +
123A THR 3.2 20.8 + - - +
124A GLY* 3.0 25.1 + - - +
125A LYS* 3.3 5.7 - - - +
126A GLY 3.2 23.1 + - - +
128A ASP* 1.3 74.7 - - - +
130A VAL* 1.3 69.0 + - + +
132A PHE* 3.4 1.6 + - - +
133A GLU* 3.1 30.5 + - - +
150A ARG* 2.9 45.0 + - - +
270A VAL* 4.4 9.1 - - - +
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Residues in contact with VAL 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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127A ASN* 3.2 10.3 + - - +
129A GLN* 1.3 82.3 - - + +
131A ARG* 1.3 65.2 + - - +
133A GLU* 3.3 3.3 + - - +
134A LEU* 3.0 42.3 + - + +
269A TYR* 4.0 15.0 - - + -
270A VAL* 3.6 31.2 - - + -
319A ASN 3.5 22.9 - - - +
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Residues in contact with ARG 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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91A TYR* 5.5 0.2 - - - -
95A THR* 3.7 14.5 - - - +
96A SER* 3.2 29.1 + - - +
99A ARG* 3.5 37.2 - - + +
100A PRO* 5.3 4.3 - - + +
103A ALA* 4.4 2.8 - - - +
127A ASN* 3.4 30.8 - - - +
128A ASP* 2.9 28.8 + - - +
130A VAL* 1.3 76.0 - - - +
132A PHE* 1.3 62.2 + - - +
134A LEU* 4.2 1.6 - - - +
135A GLY* 3.3 17.8 + - - -
317A ILE 4.7 0.2 + - - -
318A TYR* 3.0 48.0 + - - +
319A ASN 4.5 2.0 - - - +
320A GLY* 4.0 28.3 - - - +
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Residues in contact with PHE 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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11A ALA* 5.1 5.4 - - + -
99A ARG* 3.9 36.8 - - - -
102A ILE* 3.6 34.5 - - + -
103A ALA* 3.4 18.6 - - + +
106A GLN* 4.5 2.2 - - - -
120A HIS* 3.9 16.4 - + + -
122A ALA* 4.2 20.0 - - + -
128A ASP* 3.0 27.9 + - + +
129A GLN 3.8 4.0 - - - +
130A VAL 3.3 0.2 - - - -
131A ARG* 1.3 78.5 - - - +
133A GLU* 1.3 58.4 + - - +
135A GLY 3.4 0.5 + - - -
136A TYR* 3.0 60.3 + + + +
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Residues in contact with GLU 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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120A HIS* 3.0 19.6 + - - +
129A GLN 3.1 15.6 + - - +
130A VAL* 4.2 2.9 - - - +
132A PHE* 1.3 73.6 - - - +
134A LEU* 1.3 68.9 + - + +
136A TYR* 3.4 10.0 + - + +
137A LEU* 3.1 32.8 + - + +
145A ILE* 3.5 38.6 - - + +
147A ALA* 4.2 0.2 - - - +
150A ARG* 2.8 45.0 + - - -
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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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130A VAL* 3.0 41.0 + - + +
131A ARG 4.2 0.7 - - - +
133A GLU* 1.3 77.2 - - + +
135A GLY* 1.3 63.4 + - - +
137A LEU* 3.4 8.0 + - + +
138A ALA* 3.1 21.7 + - - +
319A ASN 4.2 0.2 - - - +
320A GLY 3.4 28.9 - - - +
321A TYR* 3.6 38.1 - - + +
323A PHE* 5.3 1.8 - - - +
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Residues in contact with GLY 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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100A PRO* 5.5 2.2 - - - -
103A ALA* 3.9 17.2 - - - +
131A ARG 3.3 10.8 + - - -
132A PHE 3.7 3.6 - - - -
133A GLU 3.2 0.6 - - - -
134A LEU* 1.3 76.4 - - - +
136A TYR* 1.3 65.5 + - - +
138A ALA* 3.1 20.9 + - - +
139A PHE* 3.4 13.8 - - - -
320A GLY 5.0 0.8 + - - -
323A PHE* 4.5 15.0 - - - -
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Residues in contact with TYR 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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103A ALA* 3.4 27.4 - - - -
106A GLN* 2.7 41.5 + - + -
107A ALA* 4.1 13.9 - - + +
118A VAL* 3.6 28.7 - - + -
119A SER 3.7 8.1 + - - -
120A HIS* 3.7 22.5 - + - +
132A PHE* 3.0 41.5 + - + -
133A GLU* 3.5 20.0 - - + +
135A GLY* 1.3 72.5 - - - +
137A LEU* 1.3 55.1 + - + +
139A PHE* 3.1 2.8 + - - -
140A SER* 2.7 38.7 + - - +
143A LEU* 4.6 4.9 - - + -
145A ILE* 4.1 12.6 - - + -
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Residues in contact with LEU 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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133A GLU* 3.1 19.5 + - + +
134A LEU* 4.0 7.9 - - + +
136A TYR* 1.3 78.0 - - + +
138A ALA* 1.3 63.3 + - - +
139A PHE 3.3 0.4 - - - -
140A SER 3.9 4.9 - - - +
141A PRO* 3.5 52.3 - - + +
143A LEU* 4.3 9.6 - - + +
145A ILE* 3.9 25.8 - - + -
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Residues in contact with ALA 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 10.9 + - - +
135A GLY 3.1 11.9 + - - +
137A LEU* 1.3 78.1 - - - +
139A PHE* 1.3 69.6 + - + +
141A PRO* 5.1 1.7 - - - +
323A PHE* 3.6 37.5 - - + +
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Residues in contact with PHE 139 (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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104A LYS* 3.4 48.5 - - + +
107A ALA* 3.9 18.4 - - + -
108A GLN* 4.1 15.7 - - + -
111A LEU* 3.9 13.1 - - + +
135A GLY 3.4 12.6 - - - -
136A TYR 3.1 1.6 + - - -
138A ALA* 1.3 83.6 - - + +
140A SER* 1.3 61.1 + - - +
141A PRO* 3.9 5.4 - - - +
323A PHE* 3.4 50.3 - + - -
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Residues in contact with SER 140 (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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107A ALA* 4.5 3.4 - - - -
111A LEU* 3.4 33.0 - - - +
136A TYR 2.7 17.9 + - - +
137A LEU* 3.9 3.6 - - - +
139A PHE* 1.3 76.2 - - - +
141A PRO* 1.3 59.7 - - - +
142A ASP* 3.1 6.3 + - - +
143A LEU* 3.1 54.4 + - - +
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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