Contacts of the helix formed by residues 297 - 312 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138J LYS* 4.2 10.8 - - + -
139J SER* 4.0 20.0 - - - +
295J CYS* 3.2 6.8 - - - +
296J ALA* 1.3 86.8 - - - +
298J PRO* 1.4 56.3 - - - +
299J GLY 2.7 17.0 + - - +
300J ARG* 3.1 43.2 + - + +
301J ASP* 3.1 12.3 + - - +
607M G 4.3 1.6 + - - -
608M C 3.6 32.1 - - - -
609M C 5.9 0.7 - - - -
614N G 5.7 0.2 - - - -
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Residues in contact with PRO 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139J SER* 4.9 0.7 - - - -
140J ALA* 2.9 28.9 - - + +
141J THR 3.6 12.3 - - - +
142J TRP* 4.1 1.6 - - - -
143J THR* 3.1 15.5 - - + +
152J TYR* 3.1 62.5 - - + +
153J CYS 4.1 0.4 - - - +
154J GLN* 4.0 5.4 - - - +
295J CYS* 3.2 21.7 - - - +
296J ALA 3.6 4.3 - - - +
297J CYS* 1.4 87.4 - - - +
299J GLY* 1.3 62.0 + - - +
302J ARG* 3.4 1.0 + - - +
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Residues in contact with GLY 299 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137J ALA 2.5 32.9 - - - +
138J LYS* 3.7 4.9 - - - -
139J SER 4.2 3.4 - - - +
140J ALA* 4.9 1.1 - - - +
143J THR* 4.1 4.7 - - - +
297J CYS 2.7 6.5 + - - -
298J PRO* 1.3 75.3 - - - +
300J ARG* 1.3 56.4 + - - -
302J ARG* 2.8 27.1 + - - +
303J LYS* 3.4 9.6 + - - +
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Residues in contact with ARG 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138J LYS* 3.9 39.3 - - + +
297J CYS* 3.1 29.0 + - + +
299J GLY* 1.3 72.1 - - - +
301J ASP* 1.3 74.9 + - - +
303J LYS* 3.6 7.8 + - - +
304J ALA* 3.4 19.6 + - + +
606M T 3.7 39.2 + - + +
607M G 3.0 54.0 + - - -
608M C 3.4 8.5 - - - +
615N G 4.0 4.4 + - - -
616N C 4.8 1.0 - - - +
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Residues in contact with ASP 301 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152J TYR* 3.4 12.6 - - + -
293J ARG* 2.8 42.9 + - - +
295J CYS* 3.4 12.0 - - - +
297J CYS* 3.1 14.5 + - - +
299J GLY 3.0 1.0 + - - -
300J ARG* 1.3 105.2 + - - +
302J ARG* 1.3 65.8 + - - +
304J ALA* 3.4 6.7 + - - +
305J ASP* 3.1 29.8 + - - +
606M T 4.8 5.0 - - - +
607M G 4.7 0.9 + - - -
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Residues in contact with ARG 302 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J SER* 5.0 13.3 - - - -
135J SER 5.4 3.2 + - - -
137J ALA* 6.2 2.0 - - - +
143J THR* 3.5 21.4 + - + +
144J TYR 2.6 32.4 + - - -
145J SER* 3.3 24.5 - - - +
146J PRO* 4.1 6.1 - - - +
147J LEU* 5.9 0.2 - - - +
152J TYR* 3.0 24.4 + - + -
298J PRO 3.4 11.6 + - - +
299J GLY* 2.8 13.7 + - - +
301J ASP* 1.3 72.5 - - - +
303J LYS* 1.3 61.1 + - - +
305J ASP* 4.0 0.5 - - - -
306J GLU* 3.1 53.9 + - - +
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Residues in contact with LYS 303 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299J GLY 3.4 7.0 + - - +
300J ARG* 3.8 10.5 - - - +
301J ASP 3.3 0.4 - - - -
302J ARG* 1.3 78.9 - - - +
304J ALA* 1.3 59.9 + - - +
306J GLU* 3.2 8.9 + - - +
307J ASP* 2.6 47.0 + - - +
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Residues in contact with ALA 304 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300J ARG* 3.4 12.2 + - + +
301J ASP* 3.7 10.5 - - - +
302J ARG 3.3 0.2 - - - -
303J LYS* 1.3 79.5 - - - +
305J ASP* 1.3 59.7 + - - +
307J ASP* 3.4 8.1 + - - +
308J HIS* 2.9 40.5 + - + +
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Residues in contact with ASP 305 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148J LEU* 3.6 23.5 - - + +
150J LYS* 3.0 22.2 + - - -
152J TYR* 3.6 11.5 + - - +
293J ARG* 5.4 4.3 + - - +
301J ASP* 3.1 17.5 + - - +
304J ALA* 1.3 78.7 - - - +
306J GLU* 1.3 60.6 + - - +
308J HIS* 3.3 12.8 + - - +
309J TYR* 3.0 25.6 + - - +
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Residues in contact with GLU 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145J SER* 2.4 40.0 + - - +
147J LEU* 3.8 29.3 - - + +
148J LEU* 4.6 4.5 - - + -
302J ARG* 3.1 45.8 + - + +
303J LYS* 3.7 7.4 - - - +
305J ASP* 1.3 74.4 - - - +
307J ASP* 1.3 69.9 + - - +
309J TYR* 3.1 2.8 + - - +
310J ARG* 2.9 41.0 + - + +
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Residues in contact with ASP 307 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303J LYS* 2.6 44.5 + - - +
304J ALA* 3.5 8.2 - - - +
306J GLU* 1.3 81.6 - - - +
308J HIS* 1.3 64.1 + - - +
310J ARG* 3.2 19.4 + - - +
311J GLU* 3.1 24.5 + - - +
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Residues in contact with HIS 308 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304J ALA* 2.9 31.8 + - + +
305J ASP* 3.5 17.5 - - - +
306J GLU 3.1 0.2 - - - -
307J ASP* 1.3 80.9 - - - +
309J TYR* 1.3 62.1 + - - +
311J GLU* 3.4 25.5 + - - +
312J GLN* 3.3 22.9 + - - +
605M A 5.0 14.7 + - - -
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Residues in contact with TYR 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J LEU* 3.9 36.6 - - + -
148J LEU* 4.4 22.0 - - + -
305J ASP 3.0 13.3 + - - +
306J GLU* 3.6 7.4 - - - +
308J HIS* 1.3 76.7 - - - +
310J ARG* 1.3 65.5 + - + +
312J GLN* 3.1 31.9 - - - -
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Residues in contact with ARG 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147J LEU* 5.3 15.3 - - + +
306J GLU* 2.9 34.7 + - + +
307J ASP* 3.4 22.7 + - - +
308J HIS 3.2 0.2 - - - -
309J TYR* 1.3 81.8 - - + +
311J GLU* 1.3 59.5 + - - +
312J GLN 3.5 1.6 + - - -
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Residues in contact with GLU 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307J ASP 3.1 13.4 + - - +
308J HIS* 3.6 31.5 + - - +
309J TYR 3.3 0.2 - - - -
310J ARG* 1.3 75.1 - - - +
312J GLN* 1.3 73.5 + - + +
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Residues in contact with GLN 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J HIS 3.3 9.5 + - - +
309J TYR* 3.1 31.8 + - - +
310J ARG 3.2 2.1 - - - -
311J GLU* 1.3 100.1 - - + +
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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