Contacts of the helix formed by residues 141 - 153 (chain B) in PDB entry 6V99
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 ASP 141 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B SER* 3.4 4.9 + - - -
140B MET* 1.3 70.1 - - - +
142B TYR* 1.3 62.6 + - - +
143B GLU* 2.8 25.8 + - - +
144B TYR* 3.5 28.1 + - + -
255B SER* 2.9 35.8 + - - +
257B VAL* 3.6 8.2 - - + +
297B TRP* 3.6 16.5 - - + -
7D GLN* 4.3 4.3 + - - +
11D ARG* 2.5 37.1 + - - -
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Residues in contact with TYR 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B ALA* 3.9 3.1 + - - -
53B ASN* 3.2 33.4 + - + +
54B ALA* 3.4 19.3 - - - -
57B SER* 2.8 26.0 + - - +
59B ILE* 4.3 17.0 - - + -
130B VAL* 4.4 11.4 - - + -
132B LEU* 3.5 36.2 - - + +
138B TYR* 2.7 21.7 + - - -
140B MET* 3.2 41.1 - - + -
141B ASP* 1.3 70.0 - - - +
143B GLU* 1.3 62.6 + - - +
144B TYR 3.2 0.7 - - - -
145B MET* 3.2 13.1 + - + +
146B LEU* 3.0 27.9 + - + +
208B ILE* 5.3 1.1 - - + -
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Residues in contact with GLU 143 (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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8B PRO* 3.6 13.5 - - - +
9B LEU* 2.7 39.3 + - - +
10B ALA* 2.9 32.8 + - - +
57B SER* 4.3 5.6 + - - +
141B ASP* 2.8 15.8 + - - +
142B TYR* 1.3 77.2 - - - +
144B TYR* 1.3 64.2 + - + +
146B LEU* 3.1 6.8 + - - +
147B GLN* 2.9 47.8 + - - +
6D VAL* 4.1 11.2 - - + +
7D GLN* 5.2 0.4 - - - -
8D PRO* 4.5 5.1 - - + +
11D ARG* 3.8 14.6 + - - +
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Residues in contact with TYR 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 3.7 34.3 - - + -
142B TYR 3.2 0.2 - - - -
143B GLU* 1.3 79.3 - - + +
145B MET* 1.3 61.2 + - - +
147B GLN* 3.4 8.7 + - - +
148B GLN* 3.2 22.3 + - - +
250B HIS* 4.2 8.7 - - + -
254B ASP* 4.2 16.6 - - + -
255B SER* 3.7 24.2 - - - -
6D VAL* 3.5 36.8 - - + +
7D GLN* 3.3 29.7 + - + +
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Residues in contact with MET 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B VAL* 6.2 0.4 - - - -
140B MET* 4.6 9.2 - - + -
141B ASP 4.3 0.8 + - - -
142B TYR* 3.2 15.9 + - + +
143B GLU 3.2 0.6 - - - -
144B TYR* 1.3 79.3 - - - +
146B LEU* 1.3 59.4 + - - +
148B GLN* 3.4 2.2 + - - +
149B HIS* 3.0 28.1 + - - +
157B THR* 3.1 35.9 - - + +
158B ILE 3.7 0.7 - - - -
159B GLY* 3.2 25.1 - - - +
208B ILE* 3.6 29.4 - - + +
210B VAL* 3.6 18.4 - - + -
250B HIS* 3.6 40.7 - - + +
255B SER* 5.1 1.3 - - - +
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Residues in contact with LEU 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B LEU* 3.9 17.2 - - + +
10B ALA* 3.7 36.8 - - + +
13B ALA* 4.1 7.4 - - + -
59B ILE* 5.1 1.6 - - + -
128B TYR* 4.1 27.9 - - + -
130B VAL* 3.8 26.2 - - + -
142B TYR* 3.0 23.0 + - + +
143B GLU* 3.5 11.9 - - - +
145B MET* 1.3 73.9 - - - +
147B GLN* 1.3 66.0 + - - +
148B GLN 3.3 0.2 + - - -
149B HIS* 3.3 6.0 + - + +
150B VAL* 3.2 24.3 + - - +
210B VAL* 4.1 12.8 - - + -
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Residues in contact with GLN 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PRO* 6.0 0.4 - - - +
9B LEU* 3.7 23.6 - - + +
143B GLU* 2.9 28.4 + - - +
144B TYR 3.7 5.4 - - - +
146B LEU* 1.3 76.7 - - - +
148B GLN* 1.3 57.6 + - - +
150B VAL* 3.3 1.8 - - - +
151B ASP* 2.8 47.3 + - - +
6D VAL* 2.8 55.2 + - + +
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Residues in contact with GLN 148 (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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144B TYR 3.2 14.1 + - - +
145B MET 3.9 3.1 - - - +
146B LEU 3.2 0.4 - - - -
147B GLN* 1.3 76.6 - - - +
149B HIS* 1.3 56.9 + - - +
151B ASP* 4.4 5.2 - - - +
152B SER* 2.6 49.9 + - - +
157B THR* 3.9 7.1 - - + +
248B VAL* 3.5 15.1 - - - +
249B ALA 2.9 34.8 + - - +
250B HIS* 3.3 27.8 + - + +
254B ASP* 5.4 2.6 - - - +
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Residues in contact with HIS 149 (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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128B TYR* 4.8 7.4 - + - -
145B MET 3.0 17.6 + - - +
146B LEU 3.3 4.9 + - - +
148B GLN* 1.3 77.9 - - - +
150B VAL* 1.3 60.7 + - + +
152B SER* 3.4 3.1 + - - -
153B GLY* 3.4 16.1 + - - -
154B ALA 3.1 28.9 + - - +
155B ASP 3.2 21.3 - - - -
156B VAL 4.0 0.2 - - - -
157B THR* 2.9 34.3 + - - +
210B VAL* 3.4 34.9 + - + -
211B PHE* 3.6 1.5 - - - -
212B HIS* 3.1 44.0 + + - -
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Residues in contact with VAL 150 (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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9B LEU* 4.1 19.7 - - + -
128B TYR* 4.3 20.2 - - + +
146B LEU 3.3 11.4 - - - +
147B GLN* 3.3 18.6 - - - +
149B HIS* 1.3 79.6 - - + +
151B ASP* 1.3 72.0 + - - +
152B SER 3.2 0.6 + - - -
153B GLY* 3.5 10.0 + - - +
212B HIS* 4.5 18.2 - - + +
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Residues in contact with ASP 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B GLN* 2.8 43.8 + - - +
148B GLN* 4.1 4.2 - - - +
150B VAL* 1.3 81.2 - - - +
152B SER* 1.3 58.6 + - - +
153B GLY 3.4 0.2 - - - -
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Residues in contact with SER 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148B GLN* 2.6 30.2 + - - +
149B HIS* 3.4 6.4 + - - -
151B ASP* 1.3 76.6 - - - +
153B GLY* 1.3 62.4 + - - +
154B ALA* 3.3 14.9 + - - +
246B LYS* 3.6 20.8 + - - +
248B VAL* 4.4 18.9 - - - +
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Residues in contact with GLY 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B HIS 3.4 8.3 + - - -
150B VAL* 3.5 6.9 + - - -
151B ASP 3.4 3.4 + - - -
152B SER* 1.3 77.4 - - - +
154B ALA* 1.3 66.0 + - - +
155B ASP* 3.8 5.9 + - - +
212B HIS* 5.9 3.1 - - - -
246B LYS* 4.5 7.1 - - - +
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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