Contacts of the strand formed by residues 94 - 101 (chain G) in PDB entry 5LS6
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 GLN 94 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84G SER* 3.4 0.2 - - - -
85G VAL* 3.0 38.2 + - + +
91G PHE* 3.7 26.0 - - + -
92G PRO 3.9 9.0 - - - +
93G THR* 1.3 76.9 - - - +
95G VAL* 1.3 66.8 + - - +
96G ILE* 6.1 0.2 - - + -
88H LEU* 5.3 5.1 - - - +
124H TYR* 6.2 0.2 - - - -
132H ILE 2.7 27.1 + - - -
133H ARG* 3.6 8.1 - - - +
134H LEU* 2.7 46.3 + - + +
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Residues in contact with VAL 95 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82G GLU* 3.8 40.2 - - + +
83G CYS 3.6 6.3 - - - +
84G SER* 3.9 16.4 - - - -
93G THR* 4.2 9.2 + - + +
94G GLN* 1.3 81.9 - - - +
96G ILE* 1.3 74.6 + - - +
97G PRO* 4.8 0.3 - - - +
134H LEU* 4.5 0.2 - - - -
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Residues in contact with ILE 96 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70G ILE* 4.7 6.1 - - + -
71G LEU 5.1 2.5 - - - +
72G THR* 4.4 14.8 - - + +
82G GLU* 3.2 8.5 - - - +
83G CYS 2.9 30.8 + - - +
94G GLN* 6.1 0.4 - - + -
95G VAL* 1.3 83.0 - - - +
97G PRO* 1.3 89.3 - - + +
134H LEU* 3.9 33.4 - - + +
135H LEU 3.5 22.7 - - - +
136H GLN* 4.3 2.5 - - - -
137H SER* 4.0 24.5 - - - +
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Residues in contact with PRO 97 (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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71G LEU 5.4 5.4 - - - +
72G THR* 4.9 15.7 - - + +
76G SER* 3.0 31.2 - - - +
80G THR* 3.8 15.9 - - + +
81G ARG 3.3 6.7 - - - +
82G GLU* 4.5 4.2 - - + -
83G CYS 4.7 0.4 - - - -
95G VAL 4.8 0.4 - - - +
96G ILE* 1.3 115.9 - - + +
98G LEU* 1.3 61.7 + - - +
99G LYS 3.8 2.6 + - - -
137H SER 3.8 4.3 + - - +
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Residues in contact with LEU 98 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80G THR* 4.0 17.2 - - - +
81G ARG* 2.7 43.4 + - + +
82G GLU 4.1 9.4 - - - +
83G CYS* 3.8 25.1 - - + +
97G PRO* 1.3 72.6 - - - +
99G LYS* 1.3 63.2 + - - +
100G THR* 3.9 4.5 + - - -
91H ASP* 5.4 0.4 - - - +
120H ARG* 4.4 14.8 - - - +
137H SER* 3.5 35.7 - - - +
139H VAL* 3.5 36.1 - - + -
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Residues in contact with LYS 99 (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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80G THR* 5.9 0.7 - - - -
81G ARG* 5.4 0.2 + - - -
97G PRO 3.8 2.2 + - - -
98G LEU* 1.3 74.5 - - - +
100G THR* 1.3 74.9 + - - +
101G LEU* 5.2 1.1 - - + -
137H SER 3.1 10.3 + - - +
138H TYR* 3.6 32.7 - - + -
139H VAL* 2.8 29.0 + - - +
180H MET* 3.0 37.9 - - + +
181H GLN* 5.1 8.7 - - - +
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Residues in contact with THR 100 (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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81G ARG* 4.0 17.8 + - - -
98G LEU 3.9 2.3 + - - -
99G LYS* 1.3 90.9 + - - +
101G LEU* 1.3 77.6 + - - +
102G ASN* 3.9 17.5 + - + +
139H VAL* 3.4 7.2 - - + +
141H ALA* 4.1 18.4 - - + -
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Residues in contact with LEU 101 (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 LYS* 5.2 0.9 - - + -
100G THR* 1.3 76.0 - - - +
102G ASN* 1.3 61.0 + - - +
121H VAL* 4.9 4.9 - - + -
138H TYR* 3.9 36.3 - - + +
139H VAL 2.5 25.4 + - - +
140H ASP* 3.9 4.7 - - - +
141H ALA 2.8 28.1 + - - -
147H PHE* 4.6 8.7 - - + -
165H VAL* 5.4 0.7 - - + -
173H ARG* 3.2 44.1 + - - +
175H ILE* 3.4 31.2 - - + -
181H GLN* 5.9 0.4 - - - -
182H CYS* 3.9 14.6 - - + +
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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