Contacts of the strand formed by residues 63 - 67 (chain L) in PDB entry 5XVO
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 63 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L ASP 3.2 10.3 + - - +
39L VAL* 3.4 21.1 - - + +
40L LEU 2.8 33.1 + - - +
62L ILE* 1.3 69.7 - - - +
64L VAL* 1.3 56.7 + - - +
65L LEU* 4.3 15.5 - - + -
76L LYS* 3.5 43.1 - - + +
182L LEU 5.1 0.4 - - - +
185L SER* 3.7 32.8 - - - +
186L ILE* 4.2 13.7 - - + +
189L ARG* 3.4 27.4 - - + +
248L PHE* 5.5 3.1 - - + -
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Residues in contact with VAL 64 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L LEU* 3.4 13.0 - - + +
42L LEU* 4.3 12.3 - - + -
54L LEU* 4.8 4.5 - - + -
57L LEU* 3.9 30.7 - - + -
58L ILE* 6.2 0.4 - - + -
62L ILE* 3.2 19.3 + - + +
63L LEU* 1.3 76.0 - - - +
65L LEU* 1.3 63.6 + - - +
66L PHE* 4.0 28.3 - - + -
76L LYS* 3.4 7.6 - - - +
77L ILE* 3.3 47.1 + - + +
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Residues in contact with LEU 65 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80K PHE* 4.1 11.2 - - + -
39L VAL* 4.5 16.8 - - + -
40L LEU 2.9 8.9 + - - +
41L LEU* 3.6 27.1 - - + -
42L LEU* 3.0 33.8 + - - +
63L LEU* 4.3 16.4 - - + -
64L VAL* 1.3 80.8 - - - +
66L PHE* 1.3 64.1 + - - +
73L PRO* 5.3 8.7 - - + -
75L GLY 3.7 12.3 - - - +
76L LYS* 4.5 1.8 - - + -
181L THR* 5.8 0.4 - - + -
182L LEU* 4.3 21.5 - - + -
185L SER* 3.5 29.2 - - - +
248L PHE* 6.0 1.8 - - + -
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Residues in contact with PHE 66 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K THR* 4.8 7.6 - - + -
54K LEU* 3.5 36.3 - - + -
55K LYS* 6.2 0.4 - - - +
58K ILE* 4.3 16.6 - - + -
66K PHE* 5.1 2.5 - + - -
77K ILE* 3.9 18.8 - - + -
42L LEU* 3.9 28.3 - - + -
49L LEU* 5.0 2.0 - - + -
54L LEU* 5.1 4.7 - - + -
64L VAL* 4.0 11.4 - - + -
65L LEU* 1.3 74.0 - - - +
67L CYS* 1.3 64.2 + - - +
73L PRO* 3.4 5.9 - - - +
74L ILE* 2.9 34.3 + - + -
75L GLY 2.9 25.1 + - - +
76L LYS 4.1 1.1 - - - -
77L ILE* 3.9 38.8 - - + -
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Residues in contact with CYS 67 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51K THR* 4.2 10.7 - - - +
55K LYS* 4.1 8.5 - - - +
41L LEU* 4.0 20.4 - - - -
42L LEU 3.3 16.5 + - - +
43L GLU* 3.3 31.2 - - - +
44L THR 4.7 0.9 - - - +
45L THR* 4.2 6.6 - - - +
66L PHE* 1.3 81.0 - - - +
68L ASP* 1.3 62.5 + - - +
71L ARG 3.9 10.5 - - - -
72L LEU 3.2 11.0 - - - +
73L PRO* 3.7 18.6 - - - -
74L ILE* 3.8 10.5 - - - +
178L TYR* 5.7 2.0 - - - -
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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