Contacts of the helix formed by residues 140 - 154 (chain A) in PDB entry 5KVI
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 140 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A GLY 3.6 3.0 - - - -
139A GLY* 1.3 79.5 - - - +
141A THR* 1.3 64.6 + - - -
142A ALA 3.5 1.8 - - - -
143A ALA* 3.9 3.4 - - - +
144A PHE* 3.1 24.4 + - - +
169A PRO* 4.1 1.6 - - - +
170A TYR 4.8 1.6 - - - -
172A ARG* 4.5 10.3 - - - -
205A PHE* 4.4 6.3 - - - -
259A ALA 5.0 0.2 + - - -
701A FAD 3.4 26.9 + - - -
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Residues in contact with THR 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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140A GLY* 1.3 70.1 - - - -
142A ALA* 1.3 67.0 + - - +
144A PHE* 3.4 2.8 + - - +
145A ALA* 3.1 22.9 + - - +
170A TYR 4.2 5.5 + - - -
171A MET* 4.3 2.9 - - - -
172A ARG* 4.9 1.0 + - - +
205A PHE* 3.5 30.1 - - + -
455A HIS* 3.8 16.6 + - + +
458A ALA* 3.7 11.9 - - + -
459A VAL* 3.5 31.4 - - + +
701A FAD 3.0 31.0 + - - -
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Residues in contact with ALA 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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141A THR* 1.3 78.8 - - - +
143A ALA* 1.3 62.6 + - - +
145A ALA 3.4 0.7 + - - -
146A ALA* 3.1 21.3 + - - +
257A LEU* 4.5 0.7 - - - -
259A ALA* 4.2 7.4 - - + -
436A ALA* 3.9 14.4 - - + +
437A GLY* 3.9 26.0 - - - +
458A ALA* 3.3 22.6 - - + +
462A GLY* 3.5 8.4 - - - -
701A FAD 2.9 15.4 + - - +
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Residues in contact with ALA 143 (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 LEU* 3.3 17.1 - - + +
138A GLY 2.9 33.4 - - - +
139A GLY* 4.0 3.6 - - - -
140A GLY 3.6 10.3 + - - +
141A THR 3.3 0.8 - - - -
142A ALA* 1.3 78.0 - - - +
144A PHE* 1.3 58.4 + - - +
146A ALA 3.3 1.2 + - - -
147A ALA* 2.9 25.6 + - - +
161A ILE* 4.4 9.0 - - + -
257A LEU* 4.2 7.0 - - - -
259A ALA* 3.9 14.0 - - + +
701A FAD 4.3 0.4 + - - -
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Residues in contact with PHE 144 (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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140A GLY 3.1 17.3 + - - +
141A THR 3.4 3.8 + - - +
142A ALA 3.4 0.2 - - - -
143A ALA* 1.3 76.5 - - - +
145A ALA* 1.3 68.8 + - + +
147A ALA* 3.3 9.3 + - + +
148A ARG* 3.1 54.2 + - + +
161A ILE* 4.7 4.5 - - + +
169A PRO* 4.0 8.0 - - + +
205A PHE* 3.7 43.3 - + + -
206A GLN* 3.4 28.7 - - + -
210A PHE* 4.1 11.2 - + - -
211A TYR* 3.3 29.8 - + - -
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Residues in contact with ALA 145 (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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141A THR 3.1 17.4 + - - +
142A ALA 3.8 2.9 - - - +
144A PHE* 1.3 84.3 - - + +
146A ALA* 1.3 58.9 + - - +
148A ARG* 3.4 5.7 + - - +
149A SER* 2.9 28.8 + - - -
459A VAL* 3.4 38.8 - - + +
462A GLY 4.0 2.2 - - - -
463A ARG* 3.7 13.6 - - + +
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Residues in contact with ALA 146 (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 LEU* 4.3 6.5 - - + -
142A ALA 3.1 9.4 + - - +
143A ALA 3.7 1.8 - - - +
145A ALA* 1.3 74.7 - - - +
147A ALA* 1.3 66.7 + - - +
149A SER* 3.1 2.0 + - - -
150A ILE* 2.8 30.4 + - + +
257A LEU* 3.5 31.9 - - + -
462A GLY 3.1 22.8 + - - +
465A ALA* 4.9 0.2 - - + -
466A GLY* 4.0 11.9 - - - +
469A MET* 5.2 0.7 - - - -
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Residues in contact with ALA 147 (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 LEU* 3.7 16.2 - - + +
143A ALA 2.9 18.1 + - - +
144A PHE* 3.3 7.6 + - + +
146A ALA* 1.3 76.6 - - - +
148A ARG* 1.3 63.9 + - + +
150A ILE* 3.5 3.8 + - - +
151A ARG* 3.2 28.7 + - - +
159A VAL* 4.0 10.1 - - + +
161A ILE* 4.0 6.5 - - + -
225A VAL* 3.9 29.3 - - + +
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Residues in contact with ARG 148 (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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144A PHE* 3.1 49.4 + - + +
145A ALA* 3.9 4.0 - - - +
147A ALA* 1.3 74.6 - - + +
149A SER* 1.3 65.1 + - - +
151A ARG* 3.4 7.7 + - - +
152A ALA* 3.0 24.6 + - - +
206A GLN* 4.0 17.0 - - - +
210A PHE* 3.9 31.8 - - + -
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Residues in contact with SER 149 (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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145A ALA 2.9 17.9 + - - -
146A ALA 3.1 4.2 + - - -
148A ARG* 1.3 78.9 - - - +
150A ILE* 1.3 60.9 + - - +
152A ALA* 3.3 6.4 + - - +
153A ARG* 3.2 25.5 + - - +
463A ARG* 2.7 44.1 + - - +
466A GLY* 4.2 3.1 - - - -
467A GLU* 3.2 22.0 + - - +
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Residues in contact with ILE 150 (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* 3.9 39.7 - - + -
136A LEU* 4.2 11.2 - - + -
146A ALA 2.8 25.3 + - - +
147A ALA* 3.7 4.5 - - - +
149A SER* 1.3 72.8 - - - +
151A ARG* 1.3 57.8 + - - +
153A ARG* 3.4 0.9 + - - +
154A ASP* 2.7 30.7 + - - +
157A ALA* 3.7 14.4 - - + -
159A VAL* 3.6 23.1 - - + -
466A GLY* 3.4 22.9 - - - +
469A MET* 4.1 22.0 - - + -
470A THR* 4.1 8.3 - - + -
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Residues in contact with ARG 151 (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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147A ALA 3.2 17.7 + - - +
148A ARG* 3.8 7.2 - - - +
149A SER 3.3 0.2 - - - -
150A ILE* 1.3 76.1 - - - +
152A ALA* 1.3 62.9 + - - +
154A ASP 3.8 4.3 - - - -
155A PRO* 3.3 25.1 - - - +
156A GLY 3.2 19.4 - - - +
157A ALA* 2.9 33.2 + - - +
159A VAL* 4.6 4.3 - - + -
210A PHE* 6.1 2.4 - - + -
222A ASN* 2.9 28.9 + - - +
223A GLY 3.8 1.8 + - - -
224A GLY* 3.3 22.2 - - - +
225A VAL* 3.7 21.5 - - + +
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Residues in contact with ALA 152 (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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148A ARG 3.0 16.3 + - - +
149A SER* 3.8 7.0 - - - +
150A ILE 3.3 0.2 - - - -
151A ARG* 1.3 79.8 - - - +
153A ARG* 1.3 63.5 + - + +
155A PRO* 4.0 10.9 - - - +
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Residues in contact with ARG 153 (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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149A SER 3.2 12.8 + - - +
150A ILE 4.1 1.3 - - - +
152A ALA* 1.3 81.8 - - + +
154A ASP* 1.3 58.0 + - - +
155A PRO* 3.6 6.7 - - - +
467A GLU* 3.5 34.9 + - + +
470A THR* 2.6 51.5 + - - +
471A GLY 3.9 3.0 - - - -
472A ALA* 3.7 26.7 - - - +
474A LYS* 4.6 8.9 - - - +
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Residues in contact with ASP 154 (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* 3.9 17.8 - - - -
150A ILE 2.7 16.5 + - - +
151A ARG* 3.4 7.3 - - - +
153A ARG* 1.3 74.6 - - - +
155A PRO* 1.3 77.1 - - - +
156A GLY 4.8 0.5 - - - -
157A ALA* 2.9 33.2 + - + +
470A THR* 4.1 16.1 - - + +
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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