Contacts of the helix formed by residues 138 - 146 (chain A) in PDB entry 4IKV
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 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A GLY 3.1 27.1 + - - -
85A GLY* 3.8 10.9 - - - +
88A ALA* 3.3 25.0 - - - +
94A THR* 3.7 28.4 - - - +
97A ALA* 3.6 3.2 - - - +
98A VAL* 4.3 2.7 - - + -
134A LEU 2.8 28.0 + - - +
135A LEU 4.0 0.4 - - - +
136A LYS 3.2 1.0 - - - -
137A PRO* 1.3 84.8 - - - +
139A VAL* 1.3 67.6 + - - +
140A SER 3.2 2.7 - - - -
141A SER* 3.1 22.6 + - - -
142A ILE* 3.7 3.5 + - - +
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Residues in contact with VAL 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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28A LEU* 4.4 22.0 - - + +
31A THR* 5.2 4.7 - - + -
32A GLU* 3.6 25.4 - - + +
98A VAL* 3.8 22.8 - - + +
135A LEU* 3.1 27.3 + - + +
136A LYS* 3.7 11.2 - - - +
138A ASN* 1.3 77.4 - - - +
140A SER* 1.3 65.2 + - - +
142A ILE* 3.1 19.2 + - - +
143A VAL* 3.6 6.9 + - - +
161A PHE* 3.8 24.9 - - + -
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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 LYS 4.9 3.1 + - - -
137A PRO 5.5 4.3 - - - -
138A ASN 3.2 1.6 - - - +
139A VAL* 1.3 83.3 - - - +
141A SER* 1.3 60.9 + - - +
143A VAL* 3.1 23.1 + - - +
144A GLY 3.3 6.9 + - - -
158A PHE* 3.4 15.6 - - - -
161A PHE* 3.4 17.4 - - - -
162A TYR* 2.9 31.4 + - - -
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Residues in contact with SER 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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94A THR* 3.9 20.3 - - - +
137A PRO 4.5 9.4 + - - -
138A ASN* 3.1 13.3 + - - -
140A SER* 1.3 77.2 - - - +
142A ILE* 1.3 63.1 + - - +
144A GLY* 3.7 2.6 + - - +
145A ASP* 3.3 26.0 + - - +
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Residues in contact with ILE 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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28A LEU* 3.8 19.7 - - + -
94A THR* 3.4 17.9 - - - +
95A SER* 3.7 31.2 - - - +
98A VAL* 3.9 22.7 - - + -
138A ASN 3.7 4.7 - - - +
139A VAL 3.4 11.7 - - - +
140A SER 3.1 0.6 - - - -
141A SER* 1.3 77.0 - - - +
143A VAL* 1.3 66.3 + - - +
145A ASP* 3.2 17.6 + - - +
146A MET* 3.6 9.4 - - - +
203A PHE* 4.5 10.8 - - + -
211A LEU* 4.0 17.7 - - + -
214A ALA* 4.1 21.8 - - + +
215A GLY* 4.7 1.1 - - - +
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Residues in contact with VAL 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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25A LEU* 4.5 12.6 - - + -
28A LEU* 3.5 18.1 - - + +
139A VAL 3.7 4.3 - - - +
140A SER* 3.1 27.6 - - - +
142A ILE* 1.3 78.6 - - - +
144A GLY* 1.3 61.3 + - - +
146A MET* 3.1 21.0 + - + +
147A TYR* 3.3 27.3 - - + -
157A GLY 4.7 0.7 - - - +
158A PHE* 3.9 31.9 - - + +
161A PHE* 4.1 23.8 - - + -
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Residues in contact with GLY 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 SER 3.3 10.7 + - - -
141A SER* 3.7 4.2 + - - -
142A ILE 3.3 0.4 - - - -
143A VAL* 1.3 78.2 - - - +
145A ASP* 1.3 61.4 + - - +
146A MET 3.2 0.9 + - - -
147A TYR* 3.3 11.1 + - - +
154A ARG* 2.9 44.9 + - - -
158A PHE* 3.6 11.6 - - - -
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Residues in contact with ASP 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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6A LYS* 2.9 32.4 + - - +
9A ILE* 3.7 24.1 - - + +
10A ALA* 3.8 12.0 + - - +
13A VAL* 4.5 0.5 - - - +
94A THR* 5.4 0.2 + - - -
141A SER 3.3 15.0 + - - +
142A ILE 3.2 6.2 + - - +
143A VAL 3.2 1.0 - - - -
144A GLY* 1.3 76.7 - - - +
146A MET* 1.3 61.8 + - - +
147A TYR 3.3 1.8 + - - +
214A ALA* 3.5 21.3 - - + -
215A GLY* 3.1 21.0 + - - -
217A TYR* 2.5 24.8 + - - -
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Residues in contact with MET 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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10A ALA* 3.7 6.2 - - - +
13A VAL* 4.0 20.1 - - + +
15A GLN* 3.2 26.2 + - - +
22A PRO* 4.0 14.6 - - + +
24A GLY* 3.4 33.7 - - - +
25A LEU* 3.5 25.6 - - + +
28A LEU* 4.0 2.5 - - + -
142A ILE 3.6 12.1 - - - +
143A VAL* 3.3 25.8 - - + +
144A GLY 3.1 0.6 - - - -
145A ASP* 1.3 79.7 - - - +
147A TYR* 1.3 79.0 + - + +
148A LYS 3.9 0.2 + - - -
211A LEU* 3.8 16.2 - - + -
214A ALA* 4.9 1.3 - - + -
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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