Contacts of the helix formed by residues 130 - 142 (chain A) in PDB entry 3RFU
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 GLY 130 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A ARG* 4.2 0.2 - - - +
125A VAL 4.7 1.3 - - - -
126A VAL 3.8 7.2 - - - -
129A GLY* 1.3 71.4 + - - -
131A TRP* 1.3 63.2 + - - +
132A PRO* 3.2 8.8 - - - +
133A PHE* 2.9 39.8 + - - +
134A PHE* 3.1 15.9 - - - -
195A THR* 4.7 7.9 - - - -
199A LEU* 4.2 14.1 - - - +
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Residues in contact with TRP 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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84A ARG* 4.1 4.5 - - - +
127A LEU* 3.1 28.0 + - + +
128A TRP* 3.4 10.8 - - + +
129A GLY* 3.1 5.9 - - - -
130A GLY* 1.3 76.7 - - - +
132A PRO* 1.3 74.0 - - + +
134A PHE* 3.0 34.0 + + + +
135A LYS* 3.0 39.1 + - + +
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Residues in contact with PRO 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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80A ASP* 4.8 3.6 - - - +
81A MET* 4.4 25.1 - - + -
84A ARG* 3.0 33.9 - - - +
130A GLY 3.3 6.7 - - - +
131A TRP* 1.3 97.2 - - + +
133A PHE* 1.3 65.7 + - + +
135A LYS* 3.2 15.7 + - + +
136A ARG* 2.9 44.1 + - - +
199A LEU* 5.4 0.7 - - + -
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Residues in contact with PHE 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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81A MET* 5.4 2.0 - - + -
130A GLY* 2.9 24.0 + - - +
132A PRO* 1.3 83.1 - - + +
134A PHE* 1.3 58.2 + - + +
136A ARG* 3.9 6.4 - - - -
137A GLY 3.0 22.3 + - - -
149A PHE* 3.5 24.6 - + + +
152A ILE* 4.2 21.8 - - + -
153A ALA* 3.2 15.8 - - + +
156A ILE* 5.9 0.7 - - + -
195A THR* 3.6 14.1 - - + -
198A VAL* 3.1 48.9 - - + -
199A LEU* 3.5 33.4 - - + -
202A GLN* 4.0 16.4 - - + -
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Residues in contact with PHE 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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126A VAL* 3.1 46.4 - - + -
127A LEU* 4.7 7.9 - - + -
130A GLY* 3.1 22.4 + - - -
131A TRP* 3.0 29.9 + + + +
133A PHE* 1.3 77.2 - - + +
135A LYS* 1.3 57.4 + - - +
137A GLY* 3.7 0.9 - - - -
138A TRP* 3.0 30.1 + - - +
153A ALA* 3.5 31.1 - - + +
156A ILE* 3.8 14.6 - - + -
157A GLY* 3.8 15.5 - - - -
160A TRP* 6.5 0.4 - + - -
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Residues in contact with LYS 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 TRP* 3.0 39.2 + - + +
132A PRO* 3.5 18.8 - - - +
134A PHE* 1.3 77.8 - - - +
136A ARG* 1.3 61.5 + - - +
138A TRP* 3.3 6.5 + - + +
139A GLN* 3.0 57.3 + - - +
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Residues in contact with ARG 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 GLU* 3.5 24.4 + - - -
81A MET* 3.7 20.6 - - - +
132A PRO* 2.9 25.5 + - - +
133A PHE* 4.2 1.4 - - - +
135A LYS* 1.3 80.8 - - + +
137A GLY* 1.3 52.3 + - - +
138A TRP 3.2 0.7 - - - -
139A GLN* 3.8 14.7 - - - +
140A SER* 2.7 36.6 + - - -
147A ASN* 4.4 2.2 + - - +
149A PHE* 3.5 51.9 - - + +
202A GLN* 4.4 6.7 + - - -
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Residues in contact with GLY 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 PHE 3.0 13.6 + - - -
134A PHE 3.7 2.0 - - - -
135A LYS 3.3 0.2 - - - -
136A ARG* 1.3 73.4 - - - +
138A TRP* 1.3 57.2 + - - +
140A SER* 2.8 21.2 + - - -
141A LEU* 3.1 18.0 + - - +
149A PHE* 3.5 23.3 - - - +
150A THR* 3.9 8.2 - - - -
153A ALA* 4.2 4.9 - - - -
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Residues in contact with TRP 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 PHE 3.0 17.2 + - - +
135A LYS* 3.6 7.6 - - + +
137A GLY* 1.3 76.2 - - - +
139A GLN* 1.3 65.1 + - + +
140A SER 3.2 1.1 - - - -
141A LEU* 3.1 43.4 + - + +
142A LYS* 2.9 34.9 + - + +
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Residues in contact with GLN 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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135A LYS* 3.0 46.5 + - + +
136A ARG* 3.8 16.4 - - - +
138A TRP* 1.3 82.4 - - + +
140A SER* 1.3 54.2 + - - +
142A LYS* 2.5 36.9 - - - +
143A THR* 4.4 0.3 + - - -
144A GLY* 4.3 1.4 + - - -
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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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136A ARG 2.7 24.1 + - - -
137A GLY* 2.8 12.3 + - - -
139A GLN* 1.3 75.4 - - - +
141A LEU* 1.3 60.8 + - - +
142A LYS 3.1 2.3 + - - +
144A GLY* 2.7 31.6 - - - +
145A GLN 4.2 8.8 - - - +
146A LEU* 4.5 3.0 - - - +
147A ASN* 3.7 18.6 - - - -
150A THR* 2.8 35.2 - - - +
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Residues in contact with LEU 141 (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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137A GLY 3.1 15.1 + - - +
138A TRP* 3.1 42.6 + - + +
140A SER* 1.3 83.7 + - - +
142A LYS* 1.3 63.6 + - + +
143A THR 3.5 2.6 + - - -
144A GLY 4.7 1.2 - - - +
146A LEU* 4.7 13.8 - - + +
150A THR* 6.0 0.7 - - - -
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Residues in contact with LYS 142 (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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138A TRP* 2.9 23.7 + - + +
139A GLN* 2.5 28.9 - - + +
141A LEU* 1.3 77.8 - - + +
143A THR* 1.3 86.2 + - + +
144A GLY 2.7 5.3 + - - -
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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