Contacts of the strand formed by residues 133 - 143 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126G GLU* 3.7 33.4 - - + +
127G ARG* 3.3 7.6 - - - -
128G GLN* 3.6 47.6 + - + -
132G GLY* 1.3 79.5 - - - -
134G ILE* 1.3 62.8 + - - +
139H THR 4.4 0.4 - - - -
140H ARG* 3.4 10.5 - - - +
141H LYS* 3.1 45.5 + - + +
143H THR* 5.1 16.8 - - + -
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Residues in contact with ILE 134 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124G HIS* 3.2 9.9 - - + -
126G GLU* 4.1 2.2 - - - +
127G ARG* 2.9 39.3 + - + +
129G ASP* 3.7 23.3 - - + +
133G TYR* 1.3 76.8 - - - +
135G SER* 1.3 70.9 + - - +
136G ARG* 3.6 46.2 - - + +
138H PHE* 4.4 10.5 - - + -
139H THR 3.4 21.5 - - - +
140H ARG* 3.9 24.0 - - + +
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Residues in contact with SER 135 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G HIS* 3.5 17.3 - - - -
125G GLU* 4.0 2.5 - - - -
126G GLU* 3.7 19.9 - - - +
134G ILE* 1.3 74.8 - - - +
136G ARG* 1.3 64.9 + - - +
138H PHE* 3.2 7.6 - - - +
139H THR* 3.0 48.3 + - - -
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Residues in contact with ARG 136 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G HIS* 3.7 53.5 + - - +
104G PHE* 3.9 12.8 - - + -
123G LYS* 3.4 2.9 - - - +
124G HIS* 3.1 67.7 + - + +
127G ARG* 3.9 8.1 - - - +
129G ASP* 4.7 2.6 + - - -
134G ILE* 3.6 31.8 - - + +
135G SER* 1.3 78.7 - - - +
137G CYS* 1.3 65.4 + - - +
137H CYS* 3.5 8.3 - - - +
138H PHE* 4.7 5.4 - - + -
140H ARG* 4.3 11.7 - - - +
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Residues in contact with CYS 137 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104G PHE* 4.7 0.9 - - - -
122G GLY 3.3 12.6 - - - +
123G LYS* 4.3 17.7 - - + -
136G ARG* 1.3 76.6 - - - +
138G PHE* 1.3 69.4 + - - +
136H ARG* 3.4 3.3 - - - +
137H CYS* 2.0 77.0 + - - +
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Residues in contact with PHE 138 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LEU* 4.1 18.4 - - + -
101G VAL* 3.9 22.4 - - + -
104G PHE* 3.6 34.3 - + - -
109G LEU* 4.3 6.3 - - + -
120G ILE* 3.6 18.8 - - + -
121G THR* 3.4 2.1 - - - +
122G GLY* 3.0 56.8 + - - +
137G CYS* 1.3 79.4 - - - +
139G THR* 1.3 70.2 + - - +
140G ARG* 4.0 8.1 - - + -
134H ILE* 4.0 17.9 - - + -
135H SER* 3.2 15.0 - - - +
136H ARG* 4.5 6.3 - - + +
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Residues in contact with THR 139 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119G GLU* 4.4 16.6 - - + +
120G ILE 3.4 5.8 - - - +
121G THR* 3.3 25.2 + - - +
138G PHE* 1.3 77.5 + - - +
140G ARG* 1.3 65.8 + - - +
141G LYS* 4.7 15.9 - - + +
126H GLU* 5.3 4.7 - - - +
133H TYR 4.8 0.2 - - - -
134H ILE* 3.3 3.4 - - - -
135H SER* 3.0 40.1 + - - -
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Residues in contact with ARG 140 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99G LEU* 3.8 27.3 - - - +
118G VAL 3.7 0.5 - - - +
119G GLU* 3.6 2.9 - - - -
120G ILE* 2.9 43.0 + - + +
138G PHE* 4.0 7.5 - - + -
139G THR* 1.3 74.6 - - - +
141G LYS* 1.3 72.1 + - - +
142G TYR* 3.7 29.2 - - + -
129H ASP* 2.8 42.0 + - - -
131H HIS* 3.5 23.3 + - - +
132H GLY 3.4 16.2 + - - +
133H TYR 3.4 7.4 - - - +
134H ILE* 3.3 32.1 - - + +
136H ARG* 3.9 3.6 - - - +
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Residues in contact with LYS 141 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117G VAL* 3.9 16.6 - - + -
118G VAL 3.3 4.5 - - - -
119G GLU* 4.0 35.6 + - + -
139G THR* 4.7 11.2 - - + +
140G ARG* 1.3 81.4 - - - +
142G TYR* 1.3 76.7 + - - +
126H GLU* 2.7 38.1 + - - +
132H GLY* 5.0 1.4 - - - -
133H TYR* 3.1 31.3 + - + +
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Residues in contact with TYR 142 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95G TRP* 4.3 19.3 - + + -
97G VAL* 4.1 43.7 - - + +
98G SER 4.6 8.5 + - - -
99G LEU* 5.2 5.9 - - + +
117G VAL* 3.3 6.9 - - - +
118G VAL* 2.9 38.6 + - + +
120G ILE* 4.4 17.0 - - + -
140G ARG* 3.7 30.8 - - + -
141G LYS* 1.3 82.8 - - - +
143G THR* 1.3 63.3 + - - +
144G LEU 3.6 0.7 + - - -
131H HIS* 3.5 35.5 - - - +
132H GLY* 5.9 0.2 - - - -
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Residues in contact with THR 143 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94F ARG* 6.3 0.7 - - - +
151F THR 3.1 23.4 + - - -
152F GLN* 4.0 19.7 - - + +
153F VAL 3.8 15.6 + - - -
154F SER* 3.5 22.9 - - - -
95G TRP* 4.8 7.1 + - - -
116G GLY 4.1 9.0 - - - +
117G VAL* 4.4 11.8 - - + +
142G TYR* 1.3 72.3 - - - +
144G LEU* 1.3 71.3 + - - +
145G PRO* 3.8 2.6 - - - +
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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