Contacts of the strand formed by residues 105 - 110 (chain I) in PDB entry 5HHM
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 THR 105 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7I GLN* 4.2 6.7 + - - -
8I SER 4.0 13.2 + - - -
9I PRO* 2.6 31.2 + - + +
10I GLN 3.6 1.8 - - - +
12I LEU* 4.8 5.8 - - + -
22I VAL* 3.6 35.4 - - + +
23I TYR 4.9 0.3 + - - -
86I GLY 3.4 0.7 - - - +
87I LEU* 3.4 3.4 - - - +
88I TYR* 3.0 36.6 + - + -
104I GLY* 1.4 71.4 + - - -
106I LYS* 1.3 68.1 + - - +
107I LEU* 3.4 9.0 + - + +
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Residues in contact with LYS 106 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10I GLN 2.7 16.9 + - - +
11I PHE* 3.4 31.2 - - + +
12I LEU 2.9 27.8 + - - +
85I THR* 6.6 0.2 - - - -
86I GLY* 3.7 9.9 - - - +
87I LEU* 4.0 14.8 - - + +
105I THR* 1.3 69.3 - - - +
107I LEU* 1.3 64.1 + - - +
108I SER* 4.0 16.3 + - - +
42J GLY* 6.5 1.3 - - - -
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Residues in contact with LEU 107 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I LEU* 3.4 20.4 - - + +
14I ILE* 3.9 26.5 - - + -
20I LEU* 3.9 19.7 - - + -
77I ILE* 3.6 28.7 - - + -
84I ASP 3.2 20.9 - - - +
85I THR* 3.3 5.7 - - - +
86I GLY* 2.8 41.1 + - - +
88I TYR* 3.6 13.5 - - + -
105I THR* 3.4 7.7 + - + +
106I LYS* 1.3 74.6 - - - +
108I SER* 1.4 60.8 + - - +
109I VAL* 3.9 14.4 - - + -
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Residues in contact with SER 108 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12I LEU 2.9 10.5 + - - +
13I SER* 3.4 14.9 + - - -
14I ILE* 3.1 26.2 + - - +
85I THR* 3.8 11.1 - - - +
106I LYS* 4.2 19.2 + - - +
107I LEU* 1.4 71.6 - - - +
109I VAL* 1.3 63.3 + - - +
110I LYS* 3.8 4.8 + - - -
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Residues in contact with VAL 109 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14I ILE* 3.4 30.3 - - + -
16I GLU* 3.9 20.4 - - - +
80I ALA* 4.1 8.5 - - + +
81I GLN 3.6 35.2 - - - +
82I PRO* 3.8 20.8 - - + +
84I ASP* 4.3 5.2 - - + -
85I THR* 3.4 14.8 + - - +
107I LEU* 3.9 22.4 - - + -
108I SER* 1.3 75.0 - - - +
110I LYS* 1.3 62.6 + - - +
111I PRO* 4.1 2.6 - - - +
160I VAL* 5.6 1.7 - - - +
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Residues in contact with LYS 110 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13I SER* 3.3 27.5 + - - +
14I ILE 2.7 18.0 + - - +
15I GLN* 3.4 20.8 + - - +
16I GLU* 2.9 26.8 + - - +
82I PRO* 4.8 0.9 - - - -
108I SER* 4.6 5.4 - - - +
109I VAL* 1.3 75.3 - - - +
111I PRO* 1.4 67.5 - - + +
141I SER* 2.8 39.8 + - - +
142I GLN* 4.6 7.2 + - - +
144I ASN* 4.4 11.1 + - - +
158I LYS* 3.5 19.5 - - - +
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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