Contacts of the strand formed by residues 122 - 130 (chain A) in PDB entry 4H3I
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 122 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A THR 3.8 2.5 - - - +
121A TYR* 1.3 83.4 - - - +
123A ASP* 1.3 61.9 + - - +
124A LEU* 4.7 1.9 - - + +
142A GLY* 3.0 6.2 - - - -
143A THR* 2.8 48.2 + - + +
157A ARG* 3.4 50.2 - - - +
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Residues in contact with ASP 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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121A TYR* 3.4 30.9 + - + +
122A ARG* 1.3 72.6 - - - +
124A LEU* 1.3 63.8 + - - +
125A ARG* 2.7 50.4 + - + +
140A GLU* 5.6 3.1 - - - +
141A LEU 3.5 6.9 - - - +
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Residues in contact with LEU 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 ARG* 3.6 2.4 + - + +
123A ASP* 1.3 75.2 + - - +
125A ARG* 1.3 72.8 + - - +
126A LYS* 3.2 12.1 + - + +
141A LEU* 3.1 28.0 + - + +
142A GLY* 3.7 25.4 - - - +
143A THR* 3.9 11.2 - - + -
159A ASN* 3.6 23.8 - - - +
194A LEU* 4.5 9.2 - - + -
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Residues in contact with ARG 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 ASP* 2.7 35.7 + - - +
124A LEU* 1.3 81.9 - - - +
126A LYS* 1.3 58.4 + - - +
141A LEU 4.0 0.4 + - - -
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Residues in contact with LYS 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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123A ASP* 4.7 0.2 + - - -
124A LEU* 3.2 14.0 - - + +
125A ARG* 1.3 78.8 - - - +
127A GLY* 1.3 67.9 + - - +
140A GLU* 3.8 3.5 - - - +
141A LEU* 2.8 55.0 + - + +
190A PRO* 4.3 12.6 - - + +
191A ASP* 4.9 6.1 + - - -
193A SER* 4.4 14.8 + - - -
194A LEU* 5.7 4.4 - - - +
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Residues in contact with GLY 127 (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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126A LYS* 1.3 88.5 - - - +
128A VAL* 1.3 63.4 + - - +
139A GLY 3.5 10.3 - - - -
140A GLU* 4.6 2.9 - - - -
141A LEU* 4.1 0.2 - - - +
190A PRO* 3.8 9.0 - - - +
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Residues in contact with VAL 128 (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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98A ASN* 4.9 0.9 - - - +
127A GLY* 1.3 74.8 - - - +
129A TYR* 1.3 63.0 + - - +
130A VAL* 4.2 10.5 - - + -
137A TRP* 3.7 22.1 - - + +
138A GLU* 3.4 4.7 - - - +
139A GLY 2.9 44.9 + - - +
141A LEU* 3.9 26.2 - - + -
161A ALA* 4.0 4.3 - - + -
189A ARG* 4.0 21.3 - - + +
190A PRO* 3.9 24.2 - - + -
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Residues in contact with TYR 129 (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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128A VAL* 1.3 78.2 - - - +
130A VAL* 1.3 72.3 + - - +
131A PRO* 3.7 31.7 - - + +
136A LYS* 3.5 39.3 + - + +
137A TRP 3.9 2.5 - - - -
138A GLU* 3.3 38.4 - - + +
189A ARG* 3.4 17.8 + - - +
190A PRO* 6.1 0.2 - - - +
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Residues in contact with VAL 130 (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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128A VAL* 4.2 1.6 - - + -
129A TYR* 1.3 82.0 - - - +
131A PRO* 1.3 67.3 - - + +
136A LYS* 3.0 6.6 - - - +
137A TRP* 2.9 77.6 + - + +
189A ARG* 4.1 22.7 - - + +
502A 10V 3.5 39.0 - - + +
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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