Contacts of the strand formed by residues 61 - 65 (chain L) in PDB entry 5EEY
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 ALA 61 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12L ILE* 3.8 23.3 - - + -
13L LYS 3.3 14.4 - - - +
15L LEU* 3.8 7.4 - - - -
19L VAL* 4.3 6.1 - - + -
57L VAL* 3.9 11.2 - - + -
60L LYS* 1.3 76.6 - - - +
62L TYR* 1.3 61.0 + - - +
63L ILE* 4.1 3.5 + - + +
70L ILE 4.1 0.2 - - - +
71L GLU* 3.2 6.8 - - - +
72L SER* 2.9 43.9 + - - +
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Residues in contact with TYR 62 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11L VAL 3.7 0.7 - - - +
12L ILE* 3.5 2.9 - - - -
13L LYS* 2.9 37.8 + - + +
15L LEU* 3.8 21.6 - - + +
61L ALA* 1.3 74.1 - - - +
63L ILE* 1.3 61.5 + - - +
64L GLN* 3.6 28.1 + - + -
69L VAL* 3.5 40.7 - - + +
70L ILE 3.8 3.4 - - - -
71L GLU* 4.0 22.0 - - + -
69M VAL 5.2 1.4 + - - -
70M ILE* 3.6 26.6 - - + +
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Residues in contact with ILE 63 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10L VAL* 4.8 1.3 - - + -
11L VAL 3.2 8.7 - - - +
12L ILE* 4.3 14.4 - - + -
57L VAL* 4.0 23.8 - - + -
61L ALA* 4.3 7.4 - - + +
62L TYR* 1.3 79.1 - - - +
64L GLN* 1.3 65.3 + - - +
65L THR* 4.1 21.3 + - + -
68L GLY 4.0 0.3 - - - +
69L VAL* 3.2 6.8 - - - +
70L ILE* 2.8 52.6 + - + +
72L SER* 4.2 13.0 - - - +
11V VAL* 6.1 0.7 - - + -
43V VAL* 3.9 30.3 - - + -
45V ILE* 4.4 12.3 - - + -
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Residues in contact with GLN 64 (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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10L VAL* 3.5 2.1 - - - +
11L VAL* 2.9 63.7 + - + +
62L TYR* 3.6 31.1 + - + -
63L ILE* 1.3 76.0 - - - +
65L THR* 1.3 66.1 + - - +
68L GLY 3.7 3.8 - - - +
69L VAL* 4.0 11.8 - - + +
65M THR* 4.8 1.4 + - - +
67M HIS* 4.1 28.1 + - + +
68M GLY* 4.3 7.1 + - - -
69M VAL 3.0 25.6 + - - +
70M ILE* 4.0 13.5 - - + +
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Residues in contact with THR 65 (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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9L PHE 4.7 1.8 - - - -
10L VAL* 3.7 25.6 - - + -
63L ILE* 4.1 13.4 - - + -
64L GLN* 1.3 79.9 - - - +
66L ARG* 1.3 64.9 + - - +
67L HIS* 2.9 23.4 + - - +
68L GLY* 2.9 22.4 + - - +
70L ILE* 6.1 0.9 - - + -
67M HIS* 3.8 20.8 - - - +
9V PHE* 3.9 15.0 - - + -
11V VAL* 3.9 19.5 - - + +
45V ILE* 4.7 2.7 - - + -
64V GLN* 4.6 1.3 + - - +
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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