Contacts of the strand formed by residues 130 - 138 (chain G) in PDB entry 5GJQ
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 VAL 130 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29G VAL* 4.1 6.3 - - - -
75G ALA 3.6 17.7 - - - +
76G GLY 4.9 0.2 - - - -
77G LEU 3.9 10.3 - - - +
80G ASP* 3.7 22.7 - - + -
81G ALA* 3.9 24.5 - - + -
84G LEU* 3.9 27.4 - - + +
128G TYR* 3.0 14.9 + - + +
129G GLY* 1.3 79.2 - - - +
131G GLY* 1.3 74.8 + - - +
132G LEU* 4.3 4.9 + - + -
147G THR* 4.2 4.5 + - - +
148G CYS 4.4 1.4 - - - -
149G PRO* 3.7 17.7 - - - +
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Residues in contact with GLY 131 (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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29G VAL* 3.7 13.9 - - - +
74G ILE* 3.7 1.2 - - - -
75G ALA* 2.9 37.7 + - - -
130G VAL* 1.3 75.1 - - - +
132G LEU* 1.3 68.4 + - - +
147G THR 3.2 12.1 - - - -
148G CYS* 6.1 0.2 - - - -
161G ILE* 3.8 14.0 - - - +
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Residues in contact with LEU 132 (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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72G ILE* 4.3 9.9 - - + -
73G SER 3.6 4.7 - - - +
74G ILE* 3.5 29.8 - - + -
81G ALA* 5.3 2.7 - - + -
84G LEU* 3.9 29.4 - - + -
88G MET* 4.0 24.9 - - - -
112G ILE* 4.5 4.3 - - + -
130G VAL* 4.4 7.9 - - + +
131G GLY* 1.3 84.8 - - - +
133G LEU* 1.3 64.3 + - - +
134G ILE* 4.2 22.2 - - + -
145G PHE 4.3 0.2 - - - -
146G GLN* 3.3 8.3 - - - +
147G THR* 2.9 44.6 + - - +
161G ILE* 4.0 2.6 - - - +
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Residues in contact with LEU 133 (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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35G THR* 3.7 43.1 - - + +
36G VAL* 4.0 14.8 - - - +
37G GLY* 4.0 4.7 - - - +
46G LEU* 4.0 14.5 - - + +
72G ILE* 3.3 4.2 - - - +
73G SER* 2.8 41.5 + - - +
132G LEU* 1.3 82.8 - - - +
134G ILE* 1.3 61.3 + - - +
144G ILE* 4.9 5.4 - - + -
145G PHE 3.2 9.9 - - - +
146G GLN* 4.1 17.0 - - + -
159G MET* 4.1 21.3 - - + +
160G SER* 4.4 0.4 - - - -
161G ILE* 4.0 14.6 - - + -
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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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70G ILE* 4.0 20.0 - - + -
71G GLY 3.6 9.4 - - - +
72G ILE* 3.8 15.0 - - + -
88G MET* 4.0 6.3 - - + -
105G VAL* 4.1 19.2 - - + +
108G LEU* 5.3 0.7 - - + -
109G VAL* 3.8 22.2 - - + -
112G ILE* 3.9 23.8 - - + -
132G LEU* 4.2 9.6 - - + -
133G LEU* 1.3 78.5 - - - +
135G ALA* 1.3 59.9 + - - +
136G GLY 4.1 0.2 + - - -
143G HIS 3.3 2.3 - - - +
144G ILE* 3.2 9.5 - - - +
145G PHE* 3.0 37.3 + - + +
147G THR* 4.0 18.2 - - + -
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Residues in contact with ALA 135 (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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44G ALA* 4.0 13.9 - - + +
46G LEU* 3.6 30.1 - - + -
70G ILE* 3.5 2.3 - - - +
71G GLY 2.9 32.3 + - - +
133G LEU 4.0 0.8 + - - -
134G ILE* 1.3 74.4 - - - +
136G GLY* 1.3 58.4 + - - +
143G HIS 3.3 4.7 - - - -
144G ILE* 3.7 14.1 - - + -
215G VAL* 3.9 7.6 - - + +
221G PHE* 4.3 8.0 - - + -
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Residues in contact with GLY 136 (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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44G ALA* 4.0 4.2 - - - +
69G HIS 3.1 12.1 - - - -
70G ILE* 4.2 2.0 - - - -
105G VAL* 4.1 18.8 - - - +
134G ILE 4.1 0.4 + - - -
135G ALA* 1.3 76.8 - - - +
137G TYR* 1.3 61.0 + - - +
141G GLY 4.5 0.2 - - - -
142G PRO* 3.3 4.0 - - - +
143G HIS* 2.9 33.1 + - - +
215G VAL* 3.8 8.1 - - - +
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Residues in contact with TYR 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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41G LYS 4.8 2.0 + - - -
42G THR* 3.6 23.7 - - - -
69G HIS* 3.2 30.1 + - + +
105G VAL* 4.1 2.2 - - - +
136G GLY* 1.3 73.9 - - - -
138G ASP* 1.3 77.0 + - - +
141G GLY* 3.4 21.8 - - - -
142G PRO* 3.4 31.2 - - + -
215G VAL* 4.4 6.1 - - + -
216G GLY* 4.0 22.7 - - - +
217G LYS* 3.4 33.7 - - + +
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Residues in contact with ASP 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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69G HIS* 5.0 3.8 - - + -
102G PRO* 6.6 0.4 - - + -
104G PRO* 4.0 11.7 - - + +
105G VAL* 3.2 33.1 + - + +
106G SER* 4.4 2.4 + - - -
137G TYR* 1.3 92.3 - - - +
139G ASP* 1.3 63.9 + - - +
140G MET* 2.6 30.8 + - - +
141G GLY 2.9 20.2 + - - -
143G HIS* 3.2 22.5 + - - -
81g HIS* 3.6 14.0 + - - +
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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