Contacts of the helix formed by residues 115 - 131 (chain A) in PDB entry 3RIG
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 115 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A GLY 4.8 1.8 + - - -
61A VAL* 3.1 38.2 - - - +
113A GLU 3.6 2.1 + - - +
114A PRO* 1.3 74.5 - - - +
116A ALA* 1.3 63.8 + - - +
117A GLY* 2.7 29.9 + - - -
118A HIS* 3.0 30.2 + - - -
119A ARG* 3.1 21.7 + - - +
293A CYS 5.8 0.2 - - - -
294A GLY* 5.1 4.6 + - - -
299B GLU* 6.5 0.7 - - + -
302B ALA* 3.9 6.5 - - - -
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Residues in contact with ALA 116 (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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115A ASN* 1.3 76.0 - - - +
117A GLY* 1.3 57.2 + - - +
119A ARG* 3.9 4.8 - - - +
120A ALA* 3.0 29.5 + - - +
294A GLY* 3.6 26.2 - - - +
298A PRO* 3.8 5.9 - - + +
298B PRO* 3.7 35.4 - - + +
299B GLU* 3.8 10.1 - - + +
302B ALA* 3.9 10.5 - - - +
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Residues in contact with GLY 117 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ASN* 2.7 18.5 + - - -
116A ALA* 1.3 69.9 - - - +
118A HIS* 1.3 62.8 + - - -
120A ALA* 3.3 2.3 + - - +
121A ILE* 3.0 35.2 + - - +
293A CYS* 4.0 20.2 - - - -
294A GLY* 4.1 4.2 - - - -
297A LEU* 4.1 12.5 - - - +
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Residues in contact with HIS 118 (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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60A GLY 4.8 1.0 + - - -
61A VAL* 3.1 45.2 - - + +
114A PRO* 3.9 7.9 - - + +
115A ASN* 3.0 52.5 + - - +
117A GLY* 1.3 75.2 - - - +
119A ARG* 1.4 58.5 + - - +
121A ILE* 3.4 7.1 + - - +
122A ALA* 2.9 29.5 + - - +
145A LEU* 3.6 19.7 - - + +
146A HIS* 3.8 33.7 + + - +
149A ALA* 3.7 19.6 - - + +
151A THR* 4.7 1.4 + - - -
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Residues in contact with ARG 119 (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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113A GLU* 5.0 4.6 + - - +
114A PRO* 3.9 22.3 - - + +
115A ASN 3.1 19.7 + - - +
116A ALA* 3.9 6.1 - - - +
118A HIS* 1.4 76.4 - - - +
120A ALA* 1.3 59.1 + - - +
122A ALA* 3.3 2.9 + - - +
123A GLU* 2.8 39.2 + - + +
148A LYS 4.1 5.3 + - - -
149A ALA* 3.6 35.0 + - - +
123B GLU* 4.6 12.8 - - - +
127B ARG* 3.4 44.3 - - - +
298B PRO 6.0 0.2 - - - +
302B ALA* 2.6 41.0 + - + +
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Residues in contact with ALA 120 (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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116A ALA 3.0 19.2 + - - +
117A GLY 3.3 4.0 + - - +
119A ARG* 1.3 76.6 - - - +
121A ILE* 1.3 57.9 + - - +
123A GLU* 3.8 4.3 - - - +
124A CYS* 2.9 31.9 + - - +
127A ARG* 5.7 0.2 + - - -
297A LEU 4.5 0.7 - - - -
298A PRO* 3.8 30.1 - - + -
301A LEU* 4.0 15.3 - - + +
123B GLU* 4.9 7.4 + - - +
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Residues in contact with ILE 121 (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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55A ILE* 3.9 29.2 - - + -
57A SER* 5.5 0.9 - - - -
117A GLY 3.0 22.9 + - - +
118A HIS* 3.7 3.6 - - - +
120A ALA* 1.3 74.0 - - - +
122A ALA* 1.3 64.5 + - - +
124A CYS* 3.7 2.2 - - - +
125A GLU* 3.1 23.2 + - - +
135A VAL* 4.8 2.1 - - + +
137A VAL* 3.4 31.2 - - + -
146A HIS* 3.9 23.6 - - + +
151A THR* 4.4 5.2 - - - +
248A VAL* 5.1 5.4 - - + -
297A LEU* 3.8 18.6 - - + -
301A LEU* 3.8 21.3 - - + -
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Residues in contact with ALA 122 (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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118A HIS 2.9 20.1 + - - +
119A ARG* 3.7 4.5 - - - +
121A ILE* 1.3 75.5 - - - +
123A GLU* 1.3 67.2 + - + +
125A GLU* 3.3 8.9 + - - +
126A THR* 3.1 24.3 + - - -
149A ALA* 3.2 30.7 - - + +
150A GLY 4.2 3.1 - - - +
151A THR* 3.7 23.3 + - - +
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Residues in contact with GLU 123 (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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119A ARG* 2.8 28.2 + - + +
120A ALA* 4.1 3.1 - - - +
122A ALA* 1.3 74.0 - - + +
124A CYS* 1.3 61.5 + - - +
126A THR* 3.3 15.6 + - - +
127A ARG* 2.9 39.1 + - - +
123B GLU* 3.2 51.0 - - + +
126B THR* 6.1 1.9 - - - +
127B ARG* 5.6 7.6 + - - +
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Residues in contact with CYS 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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47A PHE* 3.7 35.0 - - - -
53A ILE* 5.2 0.9 - - - -
55A ILE* 5.5 1.1 - - - -
120A ALA 2.9 19.4 + - - +
121A ILE 3.7 4.3 - - - +
123A GLU* 1.3 76.2 - - - +
125A GLU* 1.3 56.9 + - - +
127A ARG* 3.3 12.5 + - - +
128A LEU* 2.9 40.2 + - - +
135A VAL* 4.1 19.1 - - - -
301A LEU* 3.9 24.0 - - + +
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Residues in contact with GLU 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 ILE 3.1 13.0 + - - +
122A ALA 3.3 7.2 + - - +
124A CYS* 1.3 76.3 - - - +
126A THR* 1.3 58.2 + - - +
128A LEU* 3.8 0.7 - - - +
129A GLY* 2.8 29.5 + - - -
133A ARG 4.8 0.5 - - - +
135A VAL* 3.8 35.7 + - + +
137A VAL* 5.6 1.1 - - + +
150A GLY 4.5 0.5 - - - +
151A THR* 3.2 22.7 + - - +
152A LYS* 3.0 27.9 + - + +
153A ASN* 2.5 47.1 + - - +
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Residues in contact with THR 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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122A ALA 3.1 13.9 + - - -
123A GLU* 3.3 20.0 + - - +
125A GLU* 1.3 77.6 - - - +
127A ARG* 1.3 65.1 + - - +
129A GLY* 3.3 1.7 + - - -
130A LYS* 3.2 51.5 + - + +
150A GLY 5.3 3.8 + - - -
152A LYS* 5.8 6.9 - - - +
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Residues in contact with ARG 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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47A PHE* 4.1 12.3 - - - -
123A GLU* 2.9 30.9 + - - +
124A CYS* 3.9 10.4 - - - +
126A THR* 1.3 80.6 - - - +
128A LEU* 1.3 77.1 + - + +
130A LYS* 3.3 20.3 + - + +
131A GLN* 3.6 18.2 + - - +
301A LEU 2.5 30.1 + - - -
302A ALA* 3.5 10.7 + - - +
119B ARG* 3.4 51.3 - - - +
123B GLU* 5.6 1.2 + - - -
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Residues in contact with LEU 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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47A PHE* 4.2 7.2 - - + -
50A ALA 4.8 0.4 - - - +
53A ILE* 3.6 31.2 - - + -
124A CYS* 2.9 31.1 + - - +
127A ARG* 1.3 97.7 - - - +
129A GLY* 1.3 54.7 + - - +
131A GLN* 2.8 31.6 + - - +
132A GLY 3.2 0.2 + - - -
133A ARG* 2.9 69.8 + - + +
134A ARG 5.2 0.4 - - - +
135A VAL* 3.9 16.4 - - + -
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Residues in contact with GLY 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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125A GLU 2.8 17.8 + - - -
126A THR 3.6 2.7 - - - -
128A LEU* 1.3 74.7 - - - +
130A LYS* 1.3 56.3 + - - +
132A GLY* 3.0 20.1 + - - -
133A ARG 3.3 10.1 + - - -
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Residues in contact with LYS 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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126A THR* 3.2 36.6 + - + +
127A ARG* 3.7 12.1 - - + +
128A LEU 3.3 0.4 - - - -
129A GLY* 1.3 74.2 - - - +
131A GLN* 1.3 60.5 + - + +
132A GLY 3.4 0.8 + - - -
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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 ARG* 3.6 13.5 + - + +
128A LEU* 2.8 22.4 + - - +
130A LYS* 1.3 79.6 - - + +
132A GLY* 1.3 59.6 + - - -
133A ARG* 3.2 40.7 + - - +
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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