Contacts of the strand formed by residues 152 - 158 (chain D) in PDB entry 6VSU
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 LEU 152 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D ALA* 4.1 18.4 - - + +
51D LYS* 4.3 5.2 - - + +
52D GLY* 4.2 12.6 - - - +
55D VAL* 3.9 28.7 - - + -
64D SER* 3.0 19.3 - - - +
66D SER* 4.0 17.7 - - - +
115D THR* 4.0 12.3 - - - +
117D VAL* 4.9 0.2 - - + -
146D VAL* 3.8 20.6 - - + +
147D MET* 4.2 16.5 - - - +
149D GLU* 2.8 41.1 + - + +
151D PRO* 1.3 77.0 - - + +
153D ARG* 1.3 62.4 + - - +
154D PRO* 4.6 0.2 - - - +
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Residues in contact with ARG 153 (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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62D LYS* 4.4 7.3 + - - +
63D ALA* 3.4 29.0 - - + +
64D SER 2.8 6.9 + - - +
65D THR* 3.5 4.7 - - - +
66D SER 2.9 23.6 + - - +
146D VAL* 4.3 2.7 - - - -
151D PRO 4.0 7.1 + - - +
152D LEU* 1.3 78.8 - - - +
154D PRO* 1.3 71.4 - - + +
305D ASP* 2.8 32.7 + - - -
306D VAL 3.1 25.4 + - - -
307D VAL* 3.9 22.0 - - - +
340D ILE* 3.7 20.3 - - + +
342D LYS* 3.6 11.2 - - - +
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Residues in contact with PRO 154 (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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66D SER 3.6 6.3 - - - +
68D LEU* 5.5 2.5 - - + -
143D VAL* 4.0 29.6 - - + -
146D VAL* 4.2 17.9 - - + -
147D MET* 3.9 22.7 - - + -
153D ARG* 1.3 84.2 - - - +
155D LEU* 1.3 58.3 + - - +
156D VAL* 4.1 11.9 - - + -
167D VAL* 5.7 2.0 - - + -
171D VAL* 4.3 9.6 - - + -
266D TYR* 5.5 0.2 - - - -
307D VAL 3.5 16.4 - - - +
308D GLY* 3.2 26.2 - - - -
309D ALA 3.3 3.9 + - - +
340D ILE* 4.6 3.1 - - - +
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Residues in contact with LEU 155 (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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65D THR* 3.6 31.2 - - + -
66D SER 3.1 5.6 + - - +
67D LEU* 3.2 11.9 - - + +
68D LEU 3.0 20.2 + - - +
153D ARG 3.7 0.4 + - - -
154D PRO* 1.3 71.6 - - - +
156D VAL* 1.3 74.3 + - - +
157D LEU* 4.0 15.6 + - + -
309D ALA* 3.3 21.8 - - + +
311D VAL* 4.5 15.3 - - + -
333D VAL* 3.6 33.4 - - + +
336D LEU* 3.8 17.5 - - + -
337D ALA* 4.1 1.8 - - + +
340D ILE* 4.4 4.0 - - + -
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Residues in contact with VAL 156 (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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68D LEU* 3.1 26.0 - - + +
70D VAL* 3.7 14.8 - - + -
143D VAL* 4.4 9.0 - - + -
154D PRO* 4.8 7.4 - - + -
155D LEU* 1.3 76.9 - - - +
157D LEU* 1.3 62.7 + - - +
163D ILE* 3.6 30.3 - - + -
167D VAL* 3.9 31.6 - - + -
309D ALA 2.9 11.6 + - - +
310D ASP* 3.1 12.5 - - + +
311D VAL 3.0 26.0 + - - -
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Residues in contact with LEU 157 (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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67D LEU* 4.3 20.9 - - + -
68D LEU 3.0 8.8 + - - +
69D GLY* 4.2 2.7 - - - -
70D VAL* 2.9 25.6 + - - -
86D PRO* 3.6 33.8 - - + +
89D ILE* 4.2 18.8 - - + -
90D ARG* 4.2 24.2 - - + +
155D LEU* 4.2 10.5 - - + +
156D VAL* 1.3 78.4 - - - +
158D GLY* 1.3 63.6 + - - +
311D VAL* 3.7 5.4 - - + -
333D VAL* 3.6 35.2 - - + -
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Residues in contact with GLY 158 (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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70D VAL 3.9 1.3 - - - -
85D ALA* 3.2 22.0 - - - +
86D PRO* 3.6 7.0 - - - +
89D ILE* 4.3 3.3 - - - +
156D VAL 3.8 2.0 + - - -
157D LEU* 1.3 78.2 - - - +
159D GLY* 1.3 71.0 + - - -
163D ILE* 3.5 18.4 - - - +
311D VAL 2.9 18.8 + - - +
312D VAL* 4.2 3.3 - - - -
313D GLU 4.8 1.0 + - - -
314D PHE* 5.5 0.5 + - - +
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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