Contacts of the strand formed by residues 133 - 143 (chain A) in PDB entry 6GJH
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 133 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.6 31.6 - - + +
127A ARG* 3.3 4.7 - - - -
128A GLN* 3.8 42.9 + - + -
132A GLY* 1.3 77.6 - - - -
134A ILE* 1.3 64.4 + - - +
201A GOL 3.7 40.9 + - - -
139B THR 4.5 0.7 - - - -
140B ARG* 3.4 8.4 - - - +
141B LYS* 3.0 45.4 + - + -
143B THR* 4.8 10.8 - - + -
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Residues in contact with ILE 134 (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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124A HIS* 3.3 8.9 - - + -
126A GLU* 4.1 4.3 - - - +
127A ARG* 3.0 39.1 + - + +
129A ASP* 3.9 24.0 - - + +
133A TYR* 1.3 76.3 - - - +
135A SER* 1.3 70.2 + - - +
136A ARG* 3.7 42.0 - - + +
138B PHE* 4.2 11.2 - - + -
139B THR 3.3 17.0 - - - +
140B ARG* 3.9 33.0 - - + +
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Residues in contact with SER 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A HIS* 3.5 17.5 - - - -
125A GLU* 3.9 2.0 - - - -
126A GLU* 3.8 18.6 - - - +
134A ILE* 1.3 74.9 - - - +
136A ARG* 1.3 65.9 + - - +
138B PHE* 3.2 8.1 - - - +
139B THR* 2.9 49.8 + - - +
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Residues in contact with ARG 136 (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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103A HIS* 3.6 55.7 + - - -
104A PHE* 3.8 13.7 - - + -
123A LYS* 3.4 3.1 - - - +
124A HIS* 3.2 64.2 + - + +
127A ARG* 3.8 9.1 - - - +
129A ASP* 4.7 3.8 + - - -
134A ILE* 3.7 33.6 - - + +
135A SER* 1.3 80.6 - - - +
137A CYS* 1.3 64.4 + - - +
137B CYS* 3.4 9.6 - - - +
138B PHE* 4.6 5.6 - - + -
140B ARG* 4.2 12.1 - - - +
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Residues in contact with CYS 137 (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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104A PHE* 4.8 0.9 - - - -
122A GLY 3.2 11.7 - - - +
123A LYS* 4.4 14.4 - - + -
136A ARG* 1.3 78.0 - - - +
138A PHE* 1.3 68.2 + - - +
135B SER 6.1 0.2 - - - -
136B ARG* 3.5 2.6 - - - +
137B CYS* 2.0 79.5 + - - +
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Residues in contact with PHE 138 (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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99A LEU* 4.2 15.9 - - + -
101A VAL* 3.9 23.6 - - + -
104A PHE* 3.6 39.0 - + + -
109A LEU* 4.3 2.9 - - + -
120A ILE* 3.6 26.5 - - + -
121A THR* 3.4 3.1 - - - +
122A GLY* 2.9 48.9 + - - +
137A CYS* 1.3 78.2 - - - +
139A THR* 1.3 73.6 + - - +
140A ARG* 3.9 6.1 - - + -
134B ILE* 3.9 15.9 - - + -
135B SER 3.2 13.7 - - - +
136B ARG* 4.5 6.5 - - + -
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Residues in contact with THR 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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119A GLU* 3.8 32.3 - - + +
120A ILE 3.3 4.7 - - - +
121A THR* 3.4 17.5 + - - +
138A PHE* 1.3 77.5 + - - +
140A ARG* 1.3 61.6 + - - +
141A LYS* 4.6 12.2 - - - +
126B GLU* 5.3 4.5 - - - +
133B TYR 4.0 0.3 - - - +
134B ILE* 3.2 5.8 - - - +
135B SER* 3.0 41.4 + - - +
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Residues in contact with ARG 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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99A LEU* 3.9 23.6 - - + +
118A VAL 3.8 0.5 - - - +
119A GLU* 3.6 3.3 - - - +
120A ILE* 2.9 35.2 + - + +
138A PHE* 3.9 12.6 - - + -
139A THR* 1.3 73.9 - - - +
141A LYS* 1.3 70.3 + - - +
142A TYR* 3.0 38.4 - - + -
129B ASP* 2.9 40.6 + - - -
131B HIS* 3.5 22.1 + - - +
132B GLY 3.8 7.9 + - - +
133B TYR 3.4 7.0 - - - +
134B ILE* 3.7 25.9 - - + +
136B ARG* 3.6 17.2 - - - +
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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 VAL* 3.8 22.7 - - + -
118A VAL 3.2 4.3 - - - -
119A GLU* 3.7 31.1 + - + -
139A THR* 4.6 7.9 - - + +
140A ARG* 1.3 83.8 - - - +
142A TYR* 1.3 74.2 + - - +
126B GLU* 2.6 38.9 + - - +
132B GLY* 4.6 4.5 - - - -
133B TYR* 3.1 32.3 + - + +
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Residues in contact with TYR 142 (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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95A TRP* 4.3 19.7 - + + -
97A VAL* 4.0 36.8 - - + -
98A SER 4.3 6.0 + - - -
99A LEU* 4.1 17.7 - - + +
117A VAL* 3.3 8.2 - - - -
118A VAL* 2.9 41.0 + - + +
120A ILE* 3.7 29.4 - - + -
140A ARG* 3.0 34.2 - - + -
141A LYS* 1.3 80.2 - - - +
143A THR* 1.3 62.7 + - - +
144A LEU 3.7 0.2 + - - -
131B HIS* 4.2 25.3 - - + +
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Residues in contact with THR 143 (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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95A TRP* 4.5 8.9 + - - -
116A GLY 3.8 8.3 - - - +
117A VAL* 4.4 12.9 - - + +
142A TYR* 1.3 73.4 - - - +
144A LEU* 1.3 74.6 + - - +
145A PRO* 3.8 2.4 - - - +
133B TYR* 6.0 2.4 - - - -
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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