Contacts of the strand formed by residues 61 - 65 (chain K) in PDB entry 5EEZ
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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K ILE* 3.8 23.3 - - + -
13K LYS 3.1 14.8 - - - +
14K ALA* 4.2 2.2 - - - -
15K LEU* 3.8 8.4 - - - +
19K VAL* 4.3 3.8 - - + -
57K VAL* 4.1 8.1 - - + -
59K GLY 4.2 0.2 - - - +
60K LYS* 1.3 77.6 - - - +
62K TYR* 1.3 60.8 + - - +
63K ILE* 4.0 2.9 - - + -
71K GLU* 3.4 6.8 - - - +
72K SER* 2.9 43.6 + - - +
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Residues in contact with TYR 62 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J ILE* 3.7 25.5 - - + +
11K VAL 3.8 0.9 - - - +
12K ILE* 3.7 1.0 - - - -
13K LYS* 2.7 47.1 + - + +
15K LEU* 3.8 14.3 - - + +
61K ALA* 1.3 72.1 - - - +
63K ILE* 1.3 62.6 + - - +
64K GLN* 4.3 8.7 + - + -
69K VAL* 3.6 35.8 - - + +
70K ILE 4.1 2.2 - - - -
71K GLU* 3.7 28.7 - - + -
26V ARG 6.0 1.6 - - - -
50V GLU* 2.6 40.3 + - - +
51V HIS* 4.7 16.4 - + - -
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Residues in contact with ILE 63 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A VAL* 4.2 14.4 - - + -
45A ILE* 4.8 9.9 - - + -
10K VAL* 4.9 2.5 - - + -
11K VAL 3.1 12.1 - - - +
12K ILE* 4.2 19.7 - - + -
57K VAL* 3.8 29.6 - - + -
61K ALA* 4.5 2.9 - - + +
62K TYR* 1.3 80.2 - - - +
64K GLN* 1.3 66.4 - - - +
65K THR* 4.2 16.2 - - + -
68K GLY 3.9 0.3 - - - +
69K VAL* 3.3 7.3 - - - +
70K ILE* 2.9 50.9 + - + +
72K SER* 4.1 25.4 - - - +
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Residues in contact with GLN 64 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65J THR* 4.8 0.5 + - - -
67J HIS* 3.8 35.1 + - + +
68J GLY 4.8 1.9 - - - +
69J VAL 3.1 27.0 + - - +
70J ILE* 3.8 19.1 - - + +
10K VAL* 3.5 4.9 - - - +
11K VAL* 2.9 61.8 + - + +
62K TYR* 4.3 14.2 + - + -
63K ILE* 1.3 76.4 - - - +
65K THR* 1.3 65.2 + - - +
68K GLY 3.6 4.7 - - - +
69K VAL* 4.2 16.7 - - + +
50V GLU* 4.5 5.9 + - - -
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Residues in contact with THR 65 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A PHE* 3.6 25.0 - - + -
11A VAL* 3.9 15.4 - - + +
45A ILE* 4.7 4.3 - - + -
64A GLN* 4.7 0.9 + - - -
67J HIS* 3.7 20.5 + - - +
9K PHE 4.5 1.8 - - - -
10K VAL* 4.0 23.6 - - + -
63K ILE* 4.2 11.9 - - + -
64K GLN* 1.3 79.9 - - - +
66K ARG* 1.3 66.8 + - - +
67K HIS* 3.0 19.8 + - - +
68K GLY* 3.0 23.5 + - - +
70K ILE* 5.6 1.6 - - + -
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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