Contacts of the strand formed by residues 43 - 47 (chain H) 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 VAL 43 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G ILE 3.7 0.7 - - - +
56G LYS* 3.2 7.2 - - - +
57G VAL* 2.8 35.9 + - + +
63G ILE* 4.1 18.4 - - + -
70G ILE* 4.4 7.0 - - + -
71G GLU 4.1 4.3 - - - +
72G SER* 3.8 26.5 - - - +
11H VAL* 4.1 15.0 - - + -
12H ILE 3.3 7.6 - - - +
13H LYS* 4.0 20.2 - - + -
38H LEU* 4.6 0.9 - - - -
42H GLU* 1.3 81.4 - - - +
44H LEU* 1.3 62.7 + - - +
45H ILE* 4.0 26.0 - - + -
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Residues in contact with LEU 44 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24G LEU* 4.4 11.2 - - + -
54G ALA* 4.3 16.4 - - + -
55G ILE 3.5 21.5 - - - +
56G LYS* 4.1 11.7 - - + -
101G TRP* 5.5 3.8 - - + -
10H VAL 3.6 1.7 - - - +
11H VAL* 3.5 1.9 - - - -
12H ILE* 2.8 38.2 + - + +
21H VAL* 3.8 35.2 - - + -
36H GLU* 4.0 21.1 - - + -
38H LEU* 3.8 20.4 - - + +
43H VAL* 1.3 73.7 - - - +
45H ILE* 1.3 62.4 + - - +
46H ALA* 4.0 15.2 + - + -
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Residues in contact with ILE 45 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10G VAL* 4.2 18.8 - - + -
48G PHE* 3.6 23.5 - - + -
54G ALA* 3.2 3.1 - - - -
55G ILE* 2.7 61.1 + - + +
57G VAL* 4.4 11.2 - - + -
63G ILE* 4.8 9.9 - - + -
65G THR* 4.7 4.5 - - + -
9H PHE* 3.4 36.6 - - + -
10H VAL 3.5 3.6 - - - +
11H VAL* 4.3 11.7 - - + -
43H VAL* 4.0 20.9 - - + -
44H LEU* 1.3 76.6 - - - +
46H ALA* 1.3 58.5 + - - +
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Residues in contact with ALA 46 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G SER 4.0 4.0 - - - -
54G ALA* 4.0 3.8 - - + -
101G TRP* 3.9 27.8 - - + +
9H PHE* 3.2 3.9 - - - -
10H VAL* 2.8 50.1 + - + +
12H ILE* 4.8 3.1 - - + -
21H VAL* 5.1 0.2 - - + -
44H LEU* 4.2 19.5 - - + -
45H ILE* 1.3 75.0 - - - +
47H GLN* 1.3 60.8 + - - +
55H ILE* 4.2 2.9 - - + +
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Residues in contact with GLN 47 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7G SER* 5.6 1.4 + - - -
8G ASP* 5.8 2.4 - - - +
26G ARG* 2.8 32.0 + - - +
48G PHE* 3.4 40.7 - - + +
53G SER* 3.0 21.1 + - - +
101G TRP* 2.8 23.8 + - - -
7H SER* 3.8 26.8 + - - +
8H ASP 3.5 7.4 - - - +
9H PHE* 3.9 14.6 - - + -
46H ALA* 1.3 74.0 - - - +
48H PHE* 1.3 72.9 + - - +
49H THR* 3.5 5.7 - - + +
52H THR* 4.4 1.6 - - - +
55H ILE* 4.0 6.5 - - - +
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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