Contacts of the strand formed by residues 138 - 141 (chain A) in PDB entry 4HNE
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 TYR 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A PRO* 3.8 22.9 - - + -
128A GLU 3.4 7.6 - - - +
129A ARG* 3.5 49.8 + - + -
130A ILE* 3.9 6.1 - - - -
135A SER 4.4 0.9 - - - -
136A GLY 4.0 5.8 - - - -
137A SER* 1.3 75.3 - - - +
139A PHE* 1.3 61.0 + - - +
140A VAL 3.5 0.2 + - - -
150A VAL* 3.3 9.0 - - - +
151A PHE* 2.8 40.2 + - + +
153A PRO* 3.9 12.8 - - + -
156A GLU* 2.5 36.8 + - - -
220A THR* 3.4 18.4 - - - -
221A PHE* 3.6 33.0 - + + -
222A ASN 3.4 9.9 + - - -
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Residues in contact with PHE 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A PRO* 3.0 21.3 - - - +
128A GLU* 2.9 27.0 + - + +
130A ILE* 3.3 35.0 - - + +
131A TYR* 3.7 30.1 - + - -
138A TYR* 1.3 69.5 - - - +
140A VAL* 1.3 63.0 + - - +
141A LYS* 3.6 6.3 + - - +
147A ILE* 3.6 42.4 - - + -
149A ALA 3.6 0.4 - - - -
150A VAL* 3.7 23.8 - - + -
263A PHE* 4.1 15.5 - + - -
500A ADP 3.7 18.4 - + - -
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Residues in contact with VAL 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 3.5 34.1 - - + +
121A ILE* 5.5 0.7 - - + -
127A PRO* 4.1 20.6 - - + -
138A TYR 4.2 0.2 - - - +
139A PHE* 1.3 73.7 - - - +
141A LYS* 1.3 60.2 + - - +
147A ILE* 3.5 4.0 - - - +
148A ILE* 2.8 34.8 + - + -
149A ALA* 2.8 30.5 + - + +
151A PHE* 3.6 31.9 - - + +
216A LEU* 4.7 4.7 - - + -
260A PHE* 4.1 9.6 - - + -
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Residues in contact with LYS 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A ALA* 4.2 9.5 - - - -
120A ALA* 3.1 18.4 - - - +
121A ILE* 6.0 0.3 - - - +
125A ILE* 4.0 20.0 - - + +
126A PHE 3.8 16.2 + - - +
127A PRO* 4.7 4.7 - - - +
128A GLU* 2.2 48.2 + - - +
139A PHE* 3.6 4.4 + - - +
140A VAL* 1.3 81.1 - - - +
142A ASP* 1.3 67.0 + - - +
145A GLY* 3.9 22.4 + - - +
146A ARG 3.2 10.5 - - - +
147A ILE* 4.4 13.2 - - + -
148A ILE* 3.9 3.6 - - - -
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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