Contacts of the strand formed by residues 61 - 65 (chain B) in PDB entry 5EF3
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B ILE* 3.9 22.9 - - + -
13B LYS 3.3 12.8 - - - +
15B LEU* 4.0 7.7 - - - +
19B VAL* 4.1 7.6 - - + -
57B VAL* 3.9 9.9 - - + -
60B LYS* 1.4 77.1 - - - +
62B TYR* 1.3 59.8 + - - +
63B ILE* 4.0 3.5 + - + -
71B GLU* 3.3 8.3 - - - +
72B SER* 3.0 45.5 + - - +
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Residues in contact with TYR 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.7 27.2 - - + +
11B VAL 3.8 0.7 - - - +
12B ILE* 3.7 0.7 - - - -
13B LYS* 2.8 45.3 + - + +
15B LEU* 3.9 19.8 - - + +
61B ALA* 1.3 74.3 - - - +
63B ILE* 1.4 60.6 + - - +
64B GLN* 4.4 18.5 + - + -
69B VAL* 3.8 31.2 - - + +
70B ILE 4.1 0.7 - - - -
71B GLU* 4.2 21.1 - - + +
26T ARG 5.9 2.5 - - - -
50T GLU* 2.8 38.1 + - - +
51T HIS* 4.8 15.6 + + - -
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Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10B VAL* 3.6 21.8 - - + -
11B VAL 3.2 9.6 - - - +
12B ILE* 4.1 13.5 - - + -
57B VAL* 3.9 22.4 - - + -
61B ALA* 4.2 7.4 - - + -
62B TYR* 1.4 80.2 - - - +
64B GLN* 1.4 63.4 + - - +
65B THR* 4.2 9.2 - - + -
68B GLY 3.8 0.3 - - - +
69B VAL* 3.2 7.3 - - - +
70B ILE* 2.7 57.0 + - + +
72B SER* 3.8 33.4 - - - +
43C VAL* 4.3 7.4 - - + -
45C ILE* 4.7 4.5 - - + -
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Residues in contact with GLN 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A THR* 4.8 2.3 + - - +
67A HIS* 3.9 37.0 + - + +
68A GLY* 4.9 1.1 - - - +
69A VAL 3.2 26.6 + - - +
70A ILE* 3.9 18.9 - - - +
10B VAL* 3.5 1.6 - - - -
11B VAL* 2.8 65.3 + - + +
62B TYR* 4.4 17.9 + - + -
63B ILE* 1.4 76.9 - - - +
65B THR* 1.3 67.0 + - - +
68B GLY 3.7 4.3 - - - +
69B VAL* 4.5 12.4 - - + +
50T GLU* 4.7 4.9 + - - -
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Residues in contact with THR 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A HIS* 3.9 18.6 + - - +
9B PHE 4.6 2.2 - - - -
10B VAL* 3.9 28.7 - - + -
63B ILE* 4.2 8.5 - - + -
64B GLN* 1.3 80.3 - - - +
66B ARG* 1.3 66.6 + - - +
67B HIS* 2.9 22.0 + - - +
68B GLY* 2.9 24.7 + - - +
70B ILE* 5.6 2.0 - - + -
9C PHE* 3.8 17.2 - - + -
11C VAL* 4.1 20.4 - - + +
45C ILE* 4.8 3.4 - - + -
64C GLN* 4.7 1.0 + - - -
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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