Contacts of the helix formed by residues 139 - 147 (chain B) in PDB entry 4OD9
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 TYR 139 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A SER* 2.7 21.0 + - - -
138B ALA* 1.3 74.3 - - - +
140B PRO* 1.4 71.3 - - + +
141B ARG 3.1 2.8 + - - +
142B ILE* 3.4 8.0 + - - +
149B PRO* 4.5 0.2 - - - -
200B VAL* 3.8 6.9 - - + +
203B LYS* 3.3 47.3 - - + +
204B ALA* 2.9 24.2 + - - +
205B TYR 3.8 11.4 - - - -
206B TRP* 3.6 40.0 - + - -
335B ARG* 3.4 34.0 - - - +
338B ASN* 2.7 38.0 + - - +
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Residues in contact with PRO 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B TYR* 1.4 88.5 - - + +
141B ARG* 1.3 62.1 + - - +
143B SER* 3.0 21.5 + - - +
146B ASN* 4.9 7.7 + - - -
147B VAL 5.3 0.9 - - - +
148B LEU* 5.0 6.7 - - + -
149B PRO* 3.9 20.6 - - + -
152B ASP* 3.1 36.1 - - + +
335B ARG* 3.7 10.3 - - - +
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B TYR* 3.1 1.2 + - - +
140B PRO* 1.3 77.6 - - - +
142B ILE* 1.3 59.7 + - + +
143B SER 3.4 2.6 + - - +
146B ASN* 5.0 7.4 + - - +
202B ARG* 3.1 34.9 - - - +
203B LYS 3.6 25.6 - - - +
204B ALA* 4.0 11.7 - - + -
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Residues in contact with ILE 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLY 3.8 11.0 - - - +
36A SER* 3.9 8.7 - - - -
37A SER* 3.4 16.0 + - - +
38A ASN* 4.3 2.8 - - - +
138B ALA* 3.9 14.4 - - + -
139B TYR 3.4 3.6 + - - +
140B PRO 3.2 0.6 - - - -
141B ARG* 1.3 78.6 - - + +
143B SER* 1.3 63.1 + - - +
144B VAL* 3.4 8.3 + - - +
202B ARG* 5.2 4.7 - - - +
204B ALA* 3.7 31.4 - - + +
205B TYR* 3.7 45.8 - - + +
315B SER* 5.8 1.3 - - - +
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER* 3.8 19.8 + - - -
38A ASN* 3.3 20.0 + - - -
140B PRO* 3.0 20.0 + - - +
141B ARG 3.4 1.4 - - - +
142B ILE* 1.3 77.6 - - - +
144B VAL* 1.3 57.1 + - - +
145B ASN 3.5 0.3 + - - -
146B ASN* 3.0 22.9 + - - -
147B VAL* 2.7 37.6 + - - +
149B PRO* 4.5 0.2 - - - -
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Residues in contact with VAL 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASN* 2.9 38.0 + - - +
74A PHE* 4.7 3.1 - - + -
75A ASP 3.5 28.7 - - - +
76A ILE* 4.1 23.3 - - + -
77A HIS 5.7 0.7 - - - +
87A LEU* 5.9 0.2 - - - +
142B ILE 4.4 6.3 - - - +
143B SER* 1.3 70.1 - - - +
145B ASN* 1.4 80.7 + - - +
146B ASN 3.2 0.9 + - - -
147B VAL* 3.4 6.1 - - - +
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Residues in contact with ASN 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 4.0 11.3 - - - +
73A SER 3.0 26.2 + - - +
74A PHE* 3.5 16.0 - - - +
87A LEU* 3.9 9.1 - - + +
143B SER 3.5 0.4 + - - -
144B VAL* 1.4 78.9 - - - +
146B ASN* 1.4 66.5 + - - +
147B VAL* 3.2 7.2 - - + -
1E NAG 2.8 33.0 + - - +
2E NAG 3.1 28.4 + - + +
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Residues in contact with ASN 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B PRO* 4.9 9.0 + - - -
141B ARG* 5.0 6.7 + - - +
143B SER* 3.0 19.5 + - - -
145B ASN* 1.4 81.0 + - - +
147B VAL* 1.3 63.0 + - - +
148B LEU 3.6 2.1 + - - -
1E NAG 4.4 0.6 + - - -
2E NAG 3.7 40.6 + - - +
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Residues in contact with VAL 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37A SER 5.9 0.9 - - - +
38A ASN* 3.9 10.8 - - - +
39A LEU 6.2 0.7 - - - +
87A LEU* 3.9 21.5 - - + -
113B GLN* 4.5 0.2 - - - +
114B VAL* 3.4 40.6 - - + +
115B PHE* 5.3 0.9 - - - -
140B PRO* 5.2 1.1 - - - +
143B SER* 2.7 33.6 + - - +
144B VAL 3.4 14.1 - - - +
145B ASN* 3.9 1.6 - - + -
146B ASN* 1.3 75.7 - - - +
148B LEU* 1.3 72.6 + - - +
149B PRO* 3.2 6.3 - - + +
1E NAG 3.5 28.0 - - - +
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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