Contacts of the helix formed by residues 297 - 311 (chain I) in PDB entry 3VD1
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 CYS 297 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I LYS* 4.8 4.5 - - - -
139I SER* 3.9 21.1 - - - +
295I CYS* 3.7 5.3 - - - +
296I ALA* 1.3 87.6 - - - +
298I PRO* 1.3 68.8 - - - +
299I GLY 3.4 1.8 - - - -
300I ARG* 3.1 41.5 + - + +
301I ASP* 3.2 21.6 + - - +
619N G 4.3 0.6 + - - -
620N C 3.1 34.5 - - - -
621N C 6.0 0.2 - - - -
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Residues in contact with PRO 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139I SER* 4.0 3.6 - - - -
140I ALA 3.2 26.0 - - - +
141I THR 4.0 1.3 - - - +
142I TRP* 4.1 1.1 - - - -
143I THR* 3.9 10.1 - - + -
152I TYR* 3.7 25.0 - - + +
153I CYS* 4.0 7.2 - - - +
154I GLN* 3.6 29.2 - - + +
295I CYS* 3.5 13.0 - - - +
296I ALA 3.3 13.7 - - - +
297I CYS* 1.3 83.4 - - - +
299I GLY* 1.3 62.8 + - - +
301I ASP* 3.3 2.8 + - - +
302I ARG* 3.1 22.5 + - - +
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Residues in contact with GLY 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I THR* 4.2 15.3 - - - +
137I ALA 4.7 0.9 - - - -
138I LYS* 3.8 13.8 - - - +
139I SER* 3.5 16.0 - - - +
140I ALA 4.0 2.7 - - - +
143I THR* 4.0 12.7 - - - +
297I CYS 3.4 0.6 - - - -
298I PRO* 1.3 78.8 - - - +
300I ARG* 1.3 60.3 + - - +
302I ARG* 3.6 4.0 + - - +
303I LYS* 3.3 21.5 + - - +
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Residues in contact with ARG 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138I LYS* 4.5 24.0 - - + +
139I SER 3.9 5.1 - - - +
297I CYS* 3.1 37.5 + - + +
299I GLY* 1.3 76.6 - - - +
301I ASP* 1.3 69.8 + - - +
303I LYS* 3.3 6.9 + - - +
304I ALA* 2.9 30.0 + - + +
603M G 4.2 9.7 + - - -
604M C 4.7 1.8 - - - +
618N T 3.4 38.8 + - - +
619N G 2.6 52.9 + - - -
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Residues in contact with ASP 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152I TYR* 3.9 9.6 - - + -
293I ARG* 2.7 46.0 + - - +
295I CYS* 3.3 12.2 - - - +
297I CYS* 3.2 17.2 + - - +
298I PRO 3.8 2.9 - - - +
300I ARG* 1.3 95.1 + - - +
302I ARG* 1.3 60.8 + - - +
304I ALA* 3.6 8.0 - - - +
305I ASP* 2.8 37.8 + - - +
618N T 4.7 5.7 - - - +
619N G 4.7 0.2 + - - -
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Residues in contact with ARG 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ARG* 4.0 13.9 - - - +
134I SER 4.3 8.3 + - - -
136I THR* 3.9 25.7 + - - +
143I THR* 3.3 28.7 + - + -
144I TYR 2.9 22.6 + - - -
145I SER* 3.9 8.0 - - - +
146I PRO* 3.7 15.6 - - - +
152I TYR* 3.8 26.9 - - + -
298I PRO 3.1 16.0 + - - +
299I GLY* 3.8 6.5 - - - +
300I ARG 3.1 0.2 - - - -
301I ASP* 1.3 75.1 - - - +
303I LYS* 1.3 56.9 + - - +
305I ASP 3.1 0.2 + - - -
306I GLU* 2.7 75.3 + - + +
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Residues in contact with LYS 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136I THR* 5.2 8.9 - - + +
299I GLY 3.3 10.0 + - - +
300I ARG* 3.3 9.0 + - - +
302I ARG* 1.3 79.1 - - - +
304I ALA* 1.3 56.8 + - - +
306I GLU* 4.5 9.0 - - - +
307I ASP* 2.8 60.6 + - - +
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Residues in contact with ALA 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300I ARG* 2.9 21.6 + - + +
301I ASP* 3.5 11.9 - - - +
302I ARG 3.0 0.2 - - - -
303I LYS* 1.3 78.0 - - - +
305I ASP* 1.3 61.9 + - - +
307I ASP* 3.8 4.3 - - - +
308I HIS* 3.0 26.5 + - - +
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Residues in contact with ASP 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148I LEU* 3.6 16.0 - - + +
150I LYS* 3.4 16.3 + - - +
152I TYR* 2.8 29.5 + - - +
293I ARG* 4.9 3.4 + - - -
301I ASP* 2.8 20.8 + - - +
302I ARG 3.8 0.9 - - - +
304I ALA* 1.3 81.4 - - - +
306I GLU* 1.3 66.7 + - - +
307I ASP 3.2 0.2 - - - -
308I HIS* 3.1 18.7 + - - +
309I TYR* 3.2 11.6 + - - +
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Residues in contact with GLU 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ARG* 4.1 20.5 + - - +
136I THR* 5.5 2.4 - - - +
145I SER* 2.8 27.5 + - - +
147I LEU* 4.0 29.1 + - + +
148I LEU* 4.6 2.7 - - + -
302I ARG* 2.7 64.8 + - + +
303I LYS* 4.4 5.5 - - - +
305I ASP* 1.3 70.5 - - - +
307I ASP* 1.3 65.1 + - - +
309I TYR* 3.0 19.9 + - - +
310I ARG* 3.8 3.8 + - - +
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Residues in contact with ASP 307 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303I LYS* 2.8 55.0 + - - +
304I ALA* 3.8 5.4 - - - +
306I GLU* 1.3 79.5 - - - +
308I HIS* 1.3 61.9 + - - +
309I TYR 3.1 1.1 + - - -
310I ARG* 3.8 2.5 + - - +
311I GLU* 3.4 39.8 + - - +
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Residues in contact with HIS 308 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304I ALA 3.0 19.5 + - - +
305I ASP* 3.1 15.2 + - - +
307I ASP* 1.3 76.2 - - - +
309I TYR* 1.3 63.8 + - - +
311I GLU* 4.0 16.3 + - - +
312I GLN 5.1 13.8 - - - -
617N A 5.3 8.4 + - - -
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Residues in contact with TYR 309 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B LEU* 4.1 35.9 - - + +
147I LEU* 4.0 21.1 - - + -
148I LEU* 4.3 24.2 - - + -
305I ASP 3.2 8.3 + - - +
306I GLU 3.0 15.0 + - - +
308I HIS* 1.3 78.4 - - - +
310I ARG* 1.3 74.9 + - + +
311I GLU 3.1 9.5 - - - +
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Residues in contact with ARG 310 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B GLY 6.4 0.2 - - - +
241B GLU* 6.5 1.8 - - - -
242B PRO* 5.6 17.7 - - - +
306I GLU 3.8 4.8 + - - +
307I ASP* 3.8 2.8 + - - +
309I TYR* 1.3 84.7 - - + +
311I GLU* 1.3 67.8 + - + +
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Residues in contact with GLU 311 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307I ASP* 3.4 30.4 + - - +
308I HIS* 4.0 9.6 + - - +
309I TYR 3.1 11.6 - - - +
310I ARG* 1.3 85.5 - - + +
312I GLN* 1.3 68.4 + - - +
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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
------------------------------------------------------------
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