Contacts of the strand formed by residues 72 - 77 (chain Z) in PDB entry 5V09
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 LYS 72 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24Z GLY 6.2 0.4 - - - -
25Z GLN 3.2 16.2 + - - +
26Z VAL* 3.5 29.2 - - + +
27Z VAL 3.0 24.9 + - - -
67Z LEU* 5.1 1.1 - - - -
70Z GLY 3.8 1.2 + - - +
71Z ILE* 1.3 74.0 - - - +
73Z PRO* 1.3 68.4 - - + +
74Z ILE* 5.1 7.4 - - - +
143Z ASP* 3.8 23.9 + - - +
355Z LEU* 4.2 14.1 - - - +
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Residues in contact with PRO 73 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27Z VAL* 3.2 9.4 - - + +
29Z VAL* 4.6 5.8 - - + -
63Z VAL* 4.4 8.3 - - + -
66Z LEU* 3.7 34.3 - - + -
67Z LEU* 3.7 19.5 - - + -
71Z ILE* 3.1 13.7 - - + +
72Z LYS* 1.3 88.6 - - + +
74Z ILE* 1.3 63.1 + - - +
75Z LEU* 4.0 6.7 - - + -
142Z VAL* 3.2 33.8 - - + +
143Z ASP* 4.0 4.3 + - - +
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Residues in contact with ILE 74 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26Z VAL* 3.7 28.7 - - + -
27Z VAL 2.9 11.6 + - - +
28Z ALA* 3.4 6.3 - - + -
29Z VAL 3.0 23.5 + - - -
72Z LYS* 4.5 9.0 - - - +
73Z PRO* 1.3 77.2 - - - +
75Z LEU* 1.3 66.0 + - - +
76Z VAL* 3.2 16.1 + - + +
143Z ASP* 3.6 17.3 - - + +
145Z LEU* 4.7 4.7 - - + -
158Z LEU* 4.5 9.2 - - + -
163Z ILE* 4.5 4.7 - - + -
164Z VAL* 4.1 11.0 - - + -
355Z LEU* 3.8 44.2 - - + -
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Residues in contact with LEU 75 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z VAL* 3.9 21.8 - - + -
31Z THR* 3.3 19.5 - - + +
34Z TRP* 4.3 7.0 - - + -
59Z CYS* 6.0 0.7 - - + -
63Z VAL* 3.9 27.8 - - + -
73Z PRO* 4.6 7.6 - - + -
74Z ILE* 1.3 69.8 - - - +
76Z VAL* 1.3 60.5 - - - +
77Z PHE* 3.4 13.0 - - + -
133Z VAL* 4.3 19.3 - - + -
137Z ALA* 3.7 27.8 - - + -
142Z VAL* 4.3 10.5 - - + -
143Z ASP 3.1 6.8 + - - +
144Z CYS* 3.3 8.6 - - - -
145Z LEU 2.9 24.8 + - - -
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Residues in contact with VAL 76 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Z VAL 3.0 12.9 + - - +
30Z ASP* 4.2 1.6 - - - -
31Z THR* 3.2 27.2 + - - -
32Z TYR* 4.6 0.7 + - - -
74Z ILE* 3.6 17.0 - - + +
75Z LEU* 1.3 74.3 - - - +
77Z PHE* 1.3 66.5 + - - +
145Z LEU* 3.2 16.4 - - + +
147Z ALA* 4.5 0.4 - - + -
151Z ALA* 4.1 18.3 - - + +
154Z GLN* 4.0 26.5 - - + -
155Z LEU* 3.7 21.8 - - + -
158Z LEU* 3.8 23.6 - - + -
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Residues in contact with PHE 77 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31Z THR* 3.3 35.0 - - + -
32Z TYR* 3.8 14.6 - + + -
35Z LEU* 4.1 8.3 - - + -
75Z LEU* 3.4 35.2 - - + -
76Z VAL* 1.3 74.6 - - - +
78Z ASP* 1.3 62.6 + - - +
127Z HIS* 5.7 0.9 - - + +
130Z ALA* 3.8 31.0 - - + -
133Z VAL* 4.0 13.9 - - + -
134Z ILE* 3.7 30.3 - - + -
144Z CYS* 4.1 4.7 - - + -
145Z LEU 3.0 11.5 + - - -
146Z VAL* 3.7 16.8 - - + -
147Z ALA* 2.8 34.8 + - - +
151Z ALA* 4.1 5.2 - - - -
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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