Contacts of the helix formed by residues 135 - 144 (chain D) in PDB entry 2VKM
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 PRO 135 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36D SER* 3.8 25.4 - - - +
38D PHE 6.0 0.4 - - - +
120D GLY 4.6 3.4 - - - +
121D LEU 5.9 0.2 - - - -
122D ALA 4.0 12.3 - - - +
123D TYR 4.2 0.4 - - - -
124D ALA* 3.6 41.3 - - + +
127D ALA* 4.8 0.2 - - + -
133D LEU 3.3 8.1 - - - +
134D GLU* 1.3 90.8 - - + +
136D PHE* 1.3 65.9 + - - +
137D PHE* 4.6 3.1 - - + +
138D ASP* 3.2 24.9 + - - +
139D SER* 3.1 17.8 + - - -
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Residues in contact with PHE 136 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18D MET* 3.8 15.0 - - + -
36D SER 5.0 0.6 + - - -
38D PHE* 4.2 24.0 - + + +
85D VAL* 3.8 19.7 - - + -
87D ILE* 4.2 22.0 - - + -
95D VAL* 3.5 31.0 - - + -
97D ALA* 3.6 20.9 - - + -
98D ASN 5.8 0.4 + - - -
119D LEU* 3.5 35.0 - - + -
120D GLY 4.7 6.1 + - - +
121D LEU* 5.3 0.7 - - + -
134D GLU 3.8 0.4 + - - -
135D PRO* 1.3 73.2 - - - +
137D PHE* 1.3 67.0 + + + +
139D SER* 3.1 8.7 + - - -
140D LEU* 2.8 45.0 + - + -
176D ILE* 5.7 1.3 - - + -
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Residues in contact with PHE 137 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121D LEU* 4.1 32.9 - - + +
135D PRO* 3.4 2.7 - - + +
136D PHE* 1.3 84.2 - + - +
138D ASP* 1.3 64.1 + - - +
140D LEU* 3.2 14.0 + - + +
141D VAL* 2.9 48.4 + - + +
146D VAL* 4.9 0.7 - - + -
147D PRO 4.3 4.0 - - - -
148D ASN* 3.7 4.0 - - - -
149D LEU 3.4 40.2 - - - -
150D PHE* 3.8 17.5 - + + -
174D MET* 6.4 0.2 - - - -
176D ILE* 3.8 30.3 - - + -
347D ARG* 3.4 35.0 - - - +
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Residues in contact with ASP 138 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ALA 4.6 1.9 - - - +
123D TYR* 5.2 2.4 - - - -
124D ALA* 5.0 6.0 + - - +
134D GLU* 3.6 18.6 - - + +
135D PRO* 3.4 36.1 - - - +
136D PHE 3.2 0.4 - - - -
137D PHE* 1.3 79.3 - - - +
139D SER* 1.3 61.1 + - - +
141D VAL* 3.3 5.7 + - - +
142D LYS* 3.0 39.2 + - - +
347D ARG* 3.1 26.1 + - - +
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Residues in contact with SER 139 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95D VAL* 5.0 3.6 - - - -
96D ARG 4.3 9.7 + - - -
97D ALA* 4.4 12.3 - - - -
98D ASN* 4.9 0.9 + - - -
134D GLU* 2.6 31.9 + - - +
135D PRO 3.1 9.5 + - - -
136D PHE* 3.1 10.9 + - - -
138D ASP* 1.3 77.3 - - - +
140D LEU* 1.3 63.4 + - - +
142D LYS* 3.9 1.7 - - - -
143D GLN* 2.9 46.1 + - - +
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Residues in contact with LEU 140 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D ILE* 5.4 2.2 - - + -
91D PRO* 4.8 3.6 - - + -
93D VAL* 3.7 21.3 - - + -
95D VAL* 3.6 30.0 - - + +
136D PHE* 2.8 31.1 + - + +
137D PHE* 3.2 25.8 + - + +
139D SER* 1.3 77.7 - - - +
141D VAL* 1.3 56.5 + - + +
144D THR* 2.8 47.0 + - - +
146D VAL* 4.5 11.2 - - + -
176D ILE* 3.6 34.1 - - + -
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Residues in contact with VAL 141 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137D PHE* 2.9 45.0 + - + +
138D ASP* 3.8 6.1 - - - +
140D LEU* 1.3 77.3 - - + +
142D LYS* 1.3 60.6 + - + +
144D THR* 2.2 25.9 - - - +
145D HIS* 3.8 7.8 - - - -
146D VAL* 3.8 24.9 - - + +
147D PRO 4.4 0.4 - - - +
148D ASN* 3.8 26.0 - - + +
347D ARG* 6.0 0.2 - - - +
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Residues in contact with LYS 142 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312C VAL* 5.4 2.9 - - - +
313C ALA* 3.8 11.3 - - - +
134D GLU* 2.7 37.7 + - - +
138D ASP* 3.0 27.1 + - - +
139D SER* 3.9 3.1 - - - +
141D VAL* 1.3 81.3 - - + +
143D GLN* 1.3 65.6 + - + +
144D THR 3.8 1.6 - - - +
145D HIS* 4.1 5.4 + - - -
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Residues in contact with GLN 143 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ALA* 3.4 5.2 - - - +
314C THR* 3.3 28.4 + - - +
94D THR 4.6 1.3 - - - +
95D VAL* 3.4 16.1 - - + -
96D ARG* 2.9 49.9 + - - +
134D GLU* 4.7 3.0 + - - -
139D SER* 2.9 31.0 + - - +
140D LEU 4.3 0.7 - - - +
142D LYS* 1.3 80.9 - - + +
144D THR* 1.3 59.7 + - + +
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Residues in contact with THR 144 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313C ALA* 4.2 2.7 - - - -
314C THR* 4.2 15.0 - - - +
93D VAL* 3.6 37.7 - - + -
94D THR 5.1 2.2 - - - +
95D VAL* 3.7 17.9 - - + -
140D LEU* 2.8 20.1 + - + +
141D VAL 2.2 32.9 - - - +
143D GLN* 1.3 80.7 - - + +
145D HIS* 1.3 64.6 + - - +
146D VAL* 3.3 23.0 + - - +
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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