Contacts of the strand formed by residues 113 - 118 (chain E) in PDB entry 3HU1
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 ARG 113 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E LYS* 1.3 90.7 - - + +
114E ILE* 1.3 66.0 + - - +
167E GLU 4.8 0.3 - - - -
168E THR* 3.7 0.9 - - - -
169E ASP* 2.9 45.2 + - + +
170E PRO* 4.7 0.3 - - - +
180E THR* 4.4 0.4 - - - -
181E VAL* 3.5 20.1 - - + +
183E HIS* 3.3 37.3 + - + +
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Residues in contact with ILE 114 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113E ARG* 1.3 78.8 - - - +
115E HIS* 1.3 60.5 + - - +
116E VAL* 4.1 14.1 - - + -
139E PHE* 4.5 8.7 - - + -
146E ILE* 3.9 28.7 - - + -
165E VAL* 5.3 0.4 - - + -
167E GLU* 3.7 9.4 - - - +
168E THR* 3.9 8.5 - - + -
174E CYS* 3.8 28.9 - - - -
176E VAL* 4.1 11.9 - - + -
180E THR* 4.0 11.2 - - + +
181E VAL 3.0 9.9 + - - +
182E ILE* 3.9 36.6 - - + -
183E HIS* 2.9 32.1 + - - +
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Residues in contact with HIS 115 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ILE* 1.3 75.5 - - - +
116E VAL* 1.3 68.0 + - - +
117E LEU* 3.9 28.3 - - + +
165E VAL* 3.7 1.9 - - - +
166E VAL* 2.8 44.0 + - + +
167E GLU* 3.3 29.3 + - + +
183E HIS* 3.4 8.5 - - + +
185E GLU* 3.2 42.2 + - + -
186E GLY* 4.0 3.7 + - - -
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Residues in contact with VAL 116 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114E ILE* 4.4 16.2 - - + -
115E HIS* 1.3 79.6 - - - +
117E LEU* 1.3 68.3 - - - +
135E LEU* 3.7 34.8 - - + -
139E PHE* 5.5 0.2 - - + -
152E PHE* 3.9 27.6 - - + -
163E PHE* 4.6 4.9 - - + -
164E LYS 3.2 12.6 - - - +
165E VAL* 4.0 11.7 - - + -
166E VAL* 5.0 0.2 - - - -
182E ILE* 4.1 11.2 - - + -
183E HIS 2.9 16.1 + - - +
184E CYS* 3.2 26.7 - - + -
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Residues in contact with LEU 117 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115E HIS* 3.9 15.7 - - + +
116E VAL* 1.3 82.9 - - - +
118E PRO* 1.4 73.2 - - + +
163E PHE* 3.3 5.1 - - - -
164E LYS* 2.8 38.2 + - - +
166E VAL* 4.0 20.6 - - + -
184E CYS 4.2 3.1 - - - +
185E GLU 4.1 3.8 - - - +
186E GLY* 3.4 42.8 - - - +
187E GLU 3.5 17.9 - - - +
189E ILE* 4.0 23.0 - - + +
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Residues in contact with PRO 118 (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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116E VAL 5.0 0.2 - - - +
117E LEU* 1.4 92.7 - - + +
119E ILE* 1.3 63.4 + - - +
120E ASP 3.5 0.9 + - - -
123E VAL* 4.2 25.4 - - + -
130E LEU* 4.5 17.3 - - + -
161E VAL* 3.9 22.2 - - + -
162E GLU 3.3 7.0 - - - +
163E PHE* 3.8 14.5 - - + -
184E CYS* 5.5 5.4 - - + +
186E GLY 5.6 1.3 - - - +
188E PRO* 3.5 13.0 - - + +
189E ILE* 2.9 26.1 + - - -
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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