Contacts of the strand formed by residues 124 - 129 (chain E) in PDB entry 2HAK
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 124 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E ILE* 4.0 13.7 - - + -
84E ILE 3.7 12.6 - - - +
85E ASP* 4.3 7.9 - - + +
86E LYS* 3.5 7.4 - - - +
120E GLU* 3.2 4.7 - - - -
121E THR* 2.6 51.7 + - - +
123E LYS* 1.3 84.5 + - - +
125E LEU* 1.3 74.8 - - - +
126E TYR* 3.8 33.0 + - + +
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Residues in contact with LEU 125 (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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82E LYS 3.6 2.0 - - - +
83E ILE* 3.7 2.3 - - - -
84E ILE* 2.8 43.5 + - + +
86E LYS* 4.0 11.2 - - + -
97E LEU* 3.6 39.3 - - + -
98E PHE* 4.3 8.5 - - + -
101E VAL* 4.1 8.5 - - + -
118E VAL* 3.7 29.8 - - + -
119E ILE 3.6 3.4 - - - +
120E GLU* 4.0 21.5 - - + +
124E THR* 1.3 79.2 - - - +
126E TYR* 1.4 65.1 - - - +
127E LEU* 4.0 21.8 - - + -
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Residues in contact with TYR 126 (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 ILE* 3.7 49.4 - - + +
55E LEU* 5.5 2.2 - - + -
81E VAL* 4.1 10.3 - - + -
82E LYS 3.4 4.5 - - - +
83E ILE* 3.3 41.9 - - + +
118E VAL* 3.4 7.3 - - - +
119E ILE* 2.6 61.6 + - + +
121E THR* 4.6 9.6 - - + +
124E THR* 3.8 31.4 + - + +
125E LEU* 1.4 74.2 - - - +
127E LEU* 1.3 66.1 + - - +
128E VAL* 4.0 1.8 - - + -
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Residues in contact with LEU 127 (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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80E ALA 3.4 3.8 - - - +
81E VAL* 4.4 0.9 - - - -
82E LYS* 2.7 53.3 + - + +
84E ILE* 3.9 23.1 - - + -
97E LEU* 5.1 1.1 - - + -
101E VAL* 3.8 21.3 - - + -
104E MET* 3.5 29.4 - - + -
115E LEU* 4.4 10.3 - - + -
117E GLU 3.5 2.9 - - - -
118E VAL* 3.7 21.8 - - + -
125E LEU* 4.0 14.4 - - + -
126E TYR* 1.3 81.1 - - - +
128E VAL* 1.3 62.0 + - - +
129E MET* 3.6 8.3 + - - +
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Residues in contact with VAL 128 (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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53E TYR* 3.4 55.0 - - + +
79E VAL* 3.5 24.5 - - + -
80E ALA 3.4 3.1 - - - -
81E VAL* 4.4 13.0 - - + +
115E LEU* 3.3 5.7 - - - +
116E PHE* 2.7 35.2 + - + -
117E GLU* 2.8 29.8 + - + +
119E ILE* 4.3 10.8 - - + -
126E TYR 5.1 0.7 - - - -
127E LEU* 1.3 74.5 - - - +
129E MET* 1.3 56.5 + - - +
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Residues in contact with MET 129 (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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67E VAL* 6.3 0.4 - - - -
79E VAL* 3.5 5.5 - - - +
80E ALA* 2.5 55.3 + - + +
82E LYS* 4.6 23.8 - - - +
104E MET* 5.0 15.9 - - - +
113E VAL* 3.7 26.7 - - + -
114E LYS 3.2 16.4 - - - +
115E LEU* 4.3 6.5 - - + -
116E PHE* 3.4 9.2 - - - -
127E LEU* 4.2 17.9 - - - +
128E VAL* 1.3 76.7 - - - +
130E GLU* 1.3 68.8 - - - +
192E ALA* 5.3 7.6 - - + -
193E ASP* 5.4 8.5 - - - +
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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