Contacts of the strand formed by residues 120 - 126 (chain A) in PDB entry 4HYY
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 ALA 120 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A GLU* 3.5 30.0 - - + +
118A SER 2.9 4.2 - - - +
119A MET* 1.3 83.8 - - - +
121A ILE* 1.3 62.2 + - - +
122A THR* 4.0 2.5 - - - +
257A SER* 3.0 11.1 + - - -
258A GLU* 5.4 0.4 - - - -
264A VAL* 3.1 25.6 + - - +
298A THR* 3.9 25.8 - - + +
299A THR* 5.9 1.3 - - - +
163B ASN* 4.4 1.8 - - - +
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Residues in contact with ILE 121 (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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120A ALA* 1.3 77.9 - - - +
122A THR* 1.3 70.9 + - - +
250A LEU* 4.5 5.8 - - + +
253A LEU* 3.6 35.7 - - + -
254A GLN* 4.0 16.4 - - + +
257A SER* 4.4 5.4 - - - +
264A VAL* 3.3 26.2 - - + -
266A VAL* 4.3 12.6 - - + -
293A LEU* 6.0 1.3 - - + -
296A ALA* 3.8 26.7 - - + +
297A SER* 3.5 17.2 - - - +
298A THR* 2.9 32.7 + - - +
299A THR 3.5 4.3 + - - -
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Residues in contact with THR 122 (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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112A LEU* 5.0 2.9 - - + +
116A ILE* 4.0 34.6 - - + +
117A GLU* 4.1 14.2 + - - +
120A ALA* 5.1 1.9 - - - +
121A ILE* 1.3 77.3 + - - +
123A GLU* 1.3 62.1 + - - +
264A VAL 2.8 10.3 + - - -
265A PHE* 3.4 8.1 - - + -
266A VAL* 2.9 27.0 + - - +
299A THR* 3.3 22.9 + - + +
301A ILE* 3.8 28.7 - - + -
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Residues in contact with GLU 123 (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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122A THR* 1.3 77.4 - - - +
124A ALA* 1.3 60.4 + - - +
125A PHE* 3.6 15.4 - - + -
266A VAL* 3.3 18.4 - - + +
268A ASN* 3.2 29.2 - - + +
287A PRO* 4.2 0.2 - - - +
293A LEU* 3.7 10.2 - - - +
297A SER* 2.9 23.8 + - - +
299A THR 2.9 8.0 + - - +
300A ARG* 2.6 51.9 + - - -
301A ILE* 2.7 34.1 + - - +
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Residues in contact with ALA 124 (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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122A THR 4.2 0.2 - - - -
123A GLU* 1.3 74.9 - - - +
125A PHE* 1.3 61.3 + - - +
132A LYS* 4.1 6.8 - - + +
135A LEU* 4.6 5.6 - - + -
265A PHE* 3.9 26.6 - - + -
266A VAL 2.8 6.5 + - - -
267A THR* 3.1 7.3 - - - -
268A ASN 3.0 22.7 + - - -
301A ILE* 3.4 14.1 - - + +
303A LEU* 4.0 22.0 - - + -
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Residues in contact with PHE 125 (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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123A GLU* 3.6 22.2 - - + +
124A ALA* 1.3 73.9 - - - +
126A GLY* 1.3 58.5 + - - +
132A LYS* 4.3 5.2 - - - -
268A ASN* 3.2 27.1 - - + +
269A GLN 4.6 2.9 - - - +
270A MET* 3.5 22.9 - - + -
286A LYS* 5.8 0.2 - - - -
287A PRO* 3.8 31.9 - - + -
300A ARG* 4.0 23.3 - - + -
301A ILE 2.9 14.7 + - - +
302A SER* 3.7 20.0 - - - -
303A LEU* 2.9 25.4 + - - +
316A TYR* 3.5 35.9 - + + -
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Residues in contact with GLY 126 (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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125A PHE* 1.3 81.0 - - - +
127A GLU* 1.3 70.2 + - - +
130A THR* 4.4 1.6 - - - -
132A LYS* 3.5 15.5 + - - +
268A ASN 3.8 3.5 + - - +
269A GLN* 4.6 0.2 - - - -
270A MET* 3.1 26.0 + - - +
303A LEU* 3.4 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