Contacts of the helix formed by residues 134 - 149 (chain A) in PDB entry 5UM9
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 THR 134 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A LYS* 3.9 23.6 - - - +
133A VAL* 1.3 76.9 - - - +
135A LYS* 1.3 63.1 + - - +
136A GLN* 3.0 23.9 + - - +
137A HIS* 3.2 27.7 + - + +
138A ASN* 3.0 26.7 + - - +
4E T 4.4 8.3 - - + +
5E C 4.5 1.3 - - - -
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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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134A THR* 1.3 73.1 - - - +
136A GLN* 1.3 66.3 + - - +
138A ASN* 3.3 6.2 + - + -
139A ASP* 2.9 56.6 + - - +
142A LYS* 4.6 12.8 - - - +
4E T 3.4 41.9 + - + +
5E C 3.3 26.2 - - - +
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Residues in contact with GLN 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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134A THR* 3.0 23.6 + - - +
135A LYS* 1.3 79.9 + - - +
137A HIS* 1.3 58.9 + - + +
139A ASP* 3.9 7.0 - - - +
140A GLU* 2.9 46.5 + - + +
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Residues in contact with HIS 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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39A ILE* 4.3 9.9 - - + -
43A LEU* 3.7 28.2 - - + +
60A THR* 4.3 17.1 + - - -
63A HIS* 3.6 34.5 - + + -
132A LYS 3.9 11.4 - - - -
133A VAL* 3.8 9.5 - - + -
134A THR* 3.2 38.7 + - + +
135A LYS 3.2 0.4 - - - -
136A GLN* 1.3 80.9 - - + +
138A ASN* 1.3 63.5 + - - +
140A GLU* 3.8 2.7 - - - +
141A CYS* 2.9 30.3 + - - +
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Residues in contact with ASN 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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36A SER* 4.3 10.7 + - - -
39A ILE* 3.5 17.6 - - - +
85A PHE* 3.5 31.1 - - + -
86A ASN 6.0 0.2 - - - +
133A VAL* 3.7 9.6 - - - +
134A THR 3.0 16.7 + - - +
135A LYS* 3.3 9.7 + - + +
137A HIS* 1.3 76.9 - - - +
139A ASP* 1.3 59.9 + - - +
141A CYS* 3.5 2.7 + - - +
142A LYS* 2.9 41.8 + - - +
5E C 3.2 33.0 + - - +
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Residues in contact with ASP 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A LYS* 2.9 48.7 + - - +
136A GLN* 3.9 6.5 + - - +
138A ASN* 1.3 76.4 - - - +
140A GLU* 1.3 61.2 + - + +
142A LYS* 3.4 20.2 + - - +
143A HIS* 2.9 28.9 + - - +
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Residues in contact with GLU 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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59A GLU* 5.5 2.8 - - - +
60A THR 4.1 1.6 - - - +
63A HIS* 3.0 28.9 + - - +
64A LEU* 3.9 12.1 - - + +
136A GLN* 2.9 30.4 + - - +
137A HIS* 3.9 2.5 - - - +
139A ASP* 1.3 76.2 - - + +
141A CYS* 1.3 57.6 + - - +
143A HIS* 3.4 7.6 + - - +
144A LEU* 2.9 28.4 + - - +
309A PHE* 4.5 11.7 - - + -
314A LYS* 3.4 32.8 + - - -
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Residues in contact with CYS 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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39A ILE* 3.7 23.8 - - + -
63A HIS* 3.9 27.8 - - - -
64A LEU* 4.5 1.8 - - - -
67A MET* 3.7 28.2 - - + +
85A PHE* 4.3 10.5 - - + -
137A HIS 2.9 19.7 + - - +
138A ASN 3.7 4.5 - - - +
140A GLU* 1.3 74.3 - - - +
142A LYS* 1.3 66.2 + - - +
144A LEU* 3.1 6.9 + - - +
145A LEU* 2.9 30.1 + - + +
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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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85A PHE* 3.9 32.3 - - + +
135A LYS* 4.6 14.3 - - - +
138A ASN* 2.9 31.6 + - - +
139A ASP* 3.6 23.8 + - - +
141A CYS* 1.3 75.8 - - - +
143A HIS* 1.3 63.7 + - - +
145A LEU* 3.2 1.2 + - - -
146A SER* 2.9 22.7 + - - -
152A TYR* 3.4 44.7 - - + +
154A ASP* 3.0 31.2 + - - +
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Residues in contact with HIS 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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139A ASP 2.9 17.2 + - - +
140A GLU* 3.6 8.7 - - - +
142A LYS* 1.3 75.8 - - - +
144A LEU* 1.3 62.0 + - - +
146A SER* 2.6 24.1 + - - -
147A LEU* 2.9 43.8 + - + +
309A PHE* 4.0 28.0 - + + -
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Residues in contact with LEU 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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64A LEU* 3.8 36.3 - - + +
67A MET* 4.0 15.9 - - + -
68A PHE* 3.9 20.0 - - + +
140A GLU 2.9 17.0 + - - +
141A CYS* 3.5 4.3 - - - +
143A HIS* 1.3 77.6 + - - +
145A LEU* 1.3 63.4 + - - +
147A LEU* 3.1 7.8 + - - +
148A MET* 2.9 38.3 + - - +
306A LEU* 3.5 29.6 - - + -
309A PHE* 4.4 10.5 - - + -
310A MET* 3.7 20.2 - - + -
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Residues in contact with LEU 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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67A MET* 3.9 21.8 - - + -
71A THR* 4.5 3.8 - - - +
83A TYR* 3.7 55.2 - - + -
85A PHE* 4.1 12.8 - - + -
141A CYS 2.9 20.0 + - - +
142A LYS 3.6 3.8 - - - +
144A LEU* 1.3 76.0 - - - +
146A SER* 1.3 62.9 + - - +
148A MET* 2.9 18.0 + - - -
150A ILE* 3.0 46.5 + - + +
152A TYR* 4.0 19.1 - - + -
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Residues in contact with SER 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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142A LYS 2.9 13.7 + - - -
143A HIS* 2.6 30.8 + - - -
145A LEU* 1.3 75.9 - - - +
147A LEU* 1.3 63.2 + - - +
149A GLY* 3.2 12.9 + - - -
150A ILE 4.2 5.6 + - - +
152A TYR* 4.2 15.9 + - - -
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Residues in contact with LEU 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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143A HIS* 2.9 46.6 + - + +
144A LEU* 3.5 7.6 - - - +
146A SER* 1.3 79.6 + - - +
148A MET* 1.3 59.1 + - - +
149A GLY 3.4 0.4 + - - -
302A ASN* 3.0 36.1 + - + +
305A GLU* 3.6 47.6 - - + +
306A LEU* 3.8 19.9 - - + +
309A PHE* 3.9 15.0 - - + -
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Residues in contact with MET 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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68A PHE* 3.9 26.7 - - + +
71A THR* 3.8 32.8 - - + -
72A ILE* 4.1 5.8 - - + -
144A LEU* 2.9 36.9 + - - +
145A LEU* 2.9 17.6 + - - +
147A LEU* 1.3 77.2 - - - +
149A GLY* 1.3 60.6 + - - +
150A ILE* 3.3 10.3 + - + +
299A SER 3.8 3.6 - - - +
301A PRO* 3.5 23.8 - - - +
306A LEU* 4.1 20.4 - - + -
328A LEU* 3.7 30.1 - - + +
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Residues in contact with GLY 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 LEU 3.0 3.4 + - - -
146A SER* 3.2 12.3 + - - -
147A LEU 3.4 1.2 + - - -
148A MET* 1.3 77.9 - - - +
150A ILE* 1.3 62.8 + - - +
297A LYS 3.6 3.5 - - - +
298A TRP* 3.4 9.4 - - - +
299A SER* 3.1 49.8 + - - -
300A GLU 4.5 2.4 + - - -
301A PRO* 4.5 0.6 - - - +
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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