Contacts of the strand formed by residues 81 - 89 (chain E) in PDB entry 5HJD
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 PHE 81 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32E TRP* 4.0 22.9 - + - -
55E LEU* 4.0 3.8 - - + -
56E HIS* 3.7 38.6 - + + -
59E PHE* 4.0 19.1 - + - -
79E ALA 3.8 12.1 - - - -
80E GLY* 1.3 80.2 - - - +
82E ILE* 1.3 78.9 + - - +
83E LEU* 3.6 37.3 + - + -
104E LEU* 2.9 41.1 + - + +
17F ARG* 3.3 15.9 + - - +
18F KCR 4.2 20.4 - - + -
19F GLN* 4.9 5.4 - - - +
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Residues in contact with ILE 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E HIS 4.6 0.5 - - - +
81E PHE* 1.3 83.0 - - - +
83E LEU* 1.3 62.0 + - - +
84E PRO* 3.3 14.7 - - + +
101E ASP* 4.0 32.8 - - + +
102E TYR 3.6 2.0 - - - +
103E ASP* 4.0 22.9 - - + +
17F ARG* 3.7 18.1 - - - +
19F GLN* 5.1 11.3 - - - +
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Residues in contact with LEU 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34E VAL* 4.0 14.8 - - + -
53E PHE* 4.0 10.8 - - + -
54E HIS 3.5 31.2 - - - +
55E LEU* 3.6 20.4 - - + -
81E PHE* 3.6 18.3 + - + -
82E ILE* 1.3 72.8 - - - +
84E PRO* 1.3 70.2 - - - +
85E ILE* 3.3 19.9 + - + +
101E ASP* 4.6 0.7 - - - -
102E TYR* 2.6 39.1 + - + +
104E LEU* 3.6 33.7 - - + -
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Residues in contact with PRO 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54E HIS* 2.9 61.9 + - + +
82E ILE* 3.3 15.9 - - + +
83E LEU* 1.3 83.2 - - - +
85E ILE* 1.3 58.9 + - - +
86E GLU* 6.0 0.2 - - + -
99E ARG* 4.0 18.6 - - + +
100E PHE 3.5 7.4 - - - +
101E ASP* 3.7 17.9 - - - +
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Residues in contact with ILE 85 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13E LEU* 3.7 27.4 - - + -
34E VAL* 4.6 8.7 - - + -
36E VAL* 3.8 14.4 - - + -
51E VAL* 3.8 26.2 - - + -
52E VAL 3.4 5.4 - - - +
53E PHE* 4.2 19.1 - - + -
83E LEU* 3.4 24.0 - - + +
84E PRO* 1.3 74.8 - - - +
86E GLU* 1.3 65.1 + - - +
87E VAL* 4.2 4.0 - - + -
98E VAL 3.7 0.9 - - - +
99E ARG* 3.3 5.5 - - - +
100E PHE* 2.7 41.2 + - - +
102E TYR* 3.8 19.1 - - + -
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Residues in contact with GLU 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E LYS 3.9 1.0 - - - +
51E VAL* 3.3 3.6 - - - +
52E VAL* 2.7 46.0 + - + +
54E HIS* 3.1 29.2 + - + +
85E ILE* 1.3 77.8 - - - +
87E VAL* 1.3 62.6 + - - +
88E TYR* 3.1 34.8 + - + -
97E LYS* 3.3 27.4 + - + -
98E VAL 3.5 4.0 - - - +
99E ARG* 4.2 23.2 - - + +
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Residues in contact with VAL 87 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11E LEU* 4.2 23.3 - - + -
13E LEU* 5.8 0.2 - - + -
36E VAL* 4.4 11.9 - - + -
48E VAL* 4.0 33.0 - - + -
50E LYS 3.8 2.2 - - - -
51E VAL* 4.3 16.4 - - + -
85E ILE* 4.8 4.7 - - + -
86E GLU* 1.3 73.9 - - - +
88E TYR* 1.3 64.5 + - - +
89E PHE* 3.7 16.8 - - + -
97E LYS* 3.2 3.2 - - - -
98E VAL* 2.9 43.8 + - + +
100E PHE* 4.4 11.4 - - + -
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Residues in contact with TYR 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E VAL* 3.6 6.6 - - - +
49E GLU* 2.8 35.5 + - - +
50E LYS* 2.8 56.6 + - + +
52E VAL* 3.8 13.4 - - + +
86E GLU* 3.1 40.4 + - + -
87E VAL* 1.3 76.5 - - - +
89E PHE* 1.3 61.5 + - - +
96E ARG* 3.5 11.7 - - + +
97E LYS* 3.5 37.1 + - + +
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Residues in contact with PHE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E PHE* 3.2 22.0 - + - +
48E VAL* 5.2 0.2 - - + -
49E GLU* 3.8 15.3 - - - +
87E VAL* 3.7 19.3 - - + -
88E TYR* 1.3 77.9 - - - +
90E LYS* 1.3 59.5 + - - +
91E ASN* 2.8 16.8 + - + +
95E PRO* 3.2 31.4 - - + -
96E ARG* 3.2 14.2 + - - +
97E LYS* 3.6 17.7 - - - -
98E VAL* 3.6 31.6 - - + -
122E LEU* 4.1 11.0 - - + -
124E PHE* 3.6 30.3 - + - -
131E PHE* 3.6 20.2 - + + -
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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