Contacts of the helix formed by residues 123 - 136 (chain A) in PDB entry 3NYN
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 ARG 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A VAL 4.2 6.5 - - - +
122A PRO* 1.3 70.0 - - - +
124A GLN* 1.3 67.4 + - + +
126A VAL* 2.9 26.2 + - - +
127A THR* 3.4 10.5 + - - -
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Residues in contact with GLN 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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122A PRO* 3.4 2.8 - - + -
123A ARG* 1.3 79.2 - - + +
125A LEU* 1.3 63.7 + - + +
126A VAL 3.3 0.5 + - - -
127A THR* 3.5 8.8 + - - +
128A ASN* 2.9 38.7 + - - +
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Residues in contact with LEU 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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121A VAL* 5.8 1.3 - - + -
122A PRO* 3.5 41.3 + - + +
123A ARG 3.2 0.8 - - - -
124A GLN* 1.3 78.2 - - + +
126A VAL* 1.3 62.9 + - + +
128A ASN* 4.1 15.0 + - - +
129A CYS* 4.0 16.6 + - - +
144A GLU* 3.7 35.2 - - + +
145A LEU* 5.2 16.0 - - + +
147A ARG* 6.1 0.7 - - - +
148A LEU* 4.2 21.5 - - + -
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Residues in contact with VAL 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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110A LEU* 4.5 40.4 - - + +
112A HIS* 6.4 1.3 - - + -
121A VAL* 3.9 19.7 - - + +
122A PRO 3.6 16.2 - - - +
123A ARG* 2.9 12.2 + - - +
125A LEU* 1.3 78.0 - - + +
127A THR* 1.3 66.4 + - - +
128A ASN 3.3 0.7 + - - -
129A CYS* 3.3 13.9 + - - +
130A THR* 3.5 15.2 + - - +
145A LEU* 5.8 4.3 - - + -
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Residues in contact with THR 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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123A ARG 3.4 10.4 + - - -
124A GLN* 3.5 12.8 + - - -
126A VAL* 1.3 78.3 - - - +
128A ASN* 1.3 66.5 + - - +
130A THR* 3.5 9.7 + - - -
131A GLN* 3.3 28.7 + - + +
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Residues in contact with ASN 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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124A GLN* 2.9 28.8 + - - +
125A LEU* 4.1 16.6 - - - +
126A VAL 3.2 0.6 - - - -
127A THR* 1.3 80.3 - - - +
129A CYS* 1.3 52.5 + - - +
131A GLN* 3.4 10.1 + - - +
132A ARG* 2.7 38.9 + - + +
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Residues in contact with CYS 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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106A THR* 5.8 3.1 - - + -
110A LEU* 5.1 9.9 - - + -
125A LEU 4.0 8.9 + - - +
126A VAL* 3.3 9.7 + - - +
127A THR 3.3 0.6 - - - -
128A ASN* 1.3 75.3 - - - +
130A THR* 1.3 60.4 + - - +
131A GLN 3.0 1.6 - - - -
132A ARG* 4.3 4.5 - - - +
133A LEU* 2.7 38.7 + - + +
141A LEU* 3.7 38.8 - - + +
142A PHE* 4.1 22.7 - - + -
144A GLU* 6.3 2.0 - - - -
145A LEU* 4.8 10.5 - - + -
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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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106A THR* 4.6 20.5 - - + +
110A LEU* 6.1 0.5 - - - +
126A VAL* 3.5 15.8 + - - +
127A THR* 3.7 12.3 + - - -
128A ASN 3.5 0.2 - - - -
129A CYS* 1.3 77.9 - - - +
131A GLN* 1.3 60.7 + - - +
133A LEU* 4.1 5.9 - - - +
134A GLU* 3.7 29.8 + - - +
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Residues in contact with GLN 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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127A THR* 3.3 19.8 + - + +
128A ASN* 3.5 13.4 - - - +
129A CYS 3.0 0.4 - - - -
130A THR* 1.3 80.5 - - - +
132A ARG* 1.3 66.0 + - - +
133A LEU 3.2 0.9 + - - -
134A GLU* 3.6 8.4 + - - +
135A GLN* 3.6 24.7 + - - +
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Residues in contact with ARG 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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128A ASN* 2.7 23.5 + - + +
131A GLN* 1.3 73.9 - - - +
133A LEU* 1.3 62.1 + - - +
135A GLN* 3.7 19.8 - - - +
136A GLY* 3.2 30.2 + - - +
138A CYS* 3.1 38.0 - - - +
140A ASP* 5.5 1.6 + - - -
141A LEU* 3.3 24.9 - - + -
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Residues in contact with LEU 133 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR* 4.3 3.4 - - + +
99A LYS* 4.9 9.7 - - + +
102A GLY* 4.2 15.3 - - - +
103A ARG* 4.1 24.2 - - + +
106A THR* 3.5 29.4 - - + +
129A CYS* 2.7 22.2 + - + +
130A THR* 4.1 5.4 - - - +
132A ARG* 1.3 72.5 - - - +
134A GLU* 1.3 71.2 + - + +
135A GLN 3.0 1.6 + - - -
136A GLY 3.3 0.2 + - - -
137A PRO* 3.2 44.6 - - + +
141A LEU* 3.5 30.5 - - + +
142A PHE* 5.4 1.3 - - + -
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Residues in contact with GLU 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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99A LYS* 5.9 4.1 - - - +
103A ARG* 3.5 42.3 + - - +
130A THR* 3.7 21.9 + - - +
131A GLN 3.6 4.7 + - - +
133A LEU* 1.3 82.3 - - + +
135A GLN* 1.3 59.2 + - - +
137A PRO* 5.1 1.5 - - - +
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Residues in contact with GLN 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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131A GLN* 3.6 31.0 + - - +
132A ARG* 3.7 21.1 - - - +
133A LEU 3.9 0.2 - - - -
134A GLU* 1.3 81.3 - - - +
136A GLY* 1.3 60.4 + - - +
137A PRO* 4.1 3.7 - - - +
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Residues in contact with GLY 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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132A ARG* 3.2 27.0 + - - +
133A LEU 3.3 3.5 + - - -
135A GLN* 1.3 87.8 - - - +
137A PRO* 1.3 64.5 - - - +
138A CYS* 3.0 10.7 + - - +
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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