Contacts of the strand formed by residues 110 - 117 (chain G) in PDB entry 6S1M
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 LYS 110 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143E GLU* 3.8 27.0 - - + +
146E ARG* 4.3 20.8 - - - +
147E ILE* 4.2 16.0 - - - +
150E ASP* 4.4 5.4 + - - -
180E ILE* 3.7 30.7 - - + -
181E LYS 3.3 4.9 - - - -
182E LEU* 3.7 14.1 - - + -
81G CYS 6.2 0.2 - - - -
86G ASP* 6.1 0.7 - - - -
105G ALA* 3.3 36.7 + - + +
108G GLN* 3.3 3.8 - - - +
109G GLU* 1.3 88.5 + - - +
111G VAL* 1.3 71.2 + - - +
112G SER* 3.9 11.2 - - - +
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Residues in contact with VAL 111 (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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179E ASN 3.8 0.9 - - - +
180E ILE* 3.4 2.7 - - - -
181E LYS* 2.9 41.6 + - + +
102G VAL* 3.7 28.0 - - + -
103G PHE 3.4 6.1 - - - +
104G GLU* 4.3 3.6 - - + -
108G GLN* 3.2 39.5 - - + +
109G GLU 5.6 0.2 - - - -
110G LYS* 1.3 74.9 - - - +
112G SER* 1.3 67.9 + - - +
113G ASP* 5.4 3.2 - - + +
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Residues in contact with SER 112 (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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150E ASP* 5.5 0.5 + - - -
179E ASN 3.5 4.3 - - - -
180E ILE* 3.8 21.2 - - - +
81G CYS 4.6 5.2 + - - -
102G VAL* 3.2 7.3 - - - +
103G PHE* 2.7 51.1 + - - +
110G LYS* 3.9 12.6 - - - -
111G VAL* 1.3 75.9 - - - +
113G ASP* 1.3 59.7 + - - +
114G TYR* 3.4 25.9 + - - -
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Residues in contact with ASP 113 (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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178E GLY* 3.0 3.5 - - - -
179E ASN* 2.8 58.3 + - - +
181E LYS* 6.5 0.2 - - - -
91G ARG* 4.3 5.0 + - - -
100G ALA* 4.6 0.3 - - - +
101G LEU 3.5 1.9 - - - +
102G VAL* 3.2 27.5 - - + +
111G VAL* 5.4 3.4 - - + +
112G SER* 1.3 75.6 - - - +
114G TYR* 1.3 61.9 + - - +
115G GLU* 2.9 31.7 - - - +
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Residues in contact with TYR 114 (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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150E ASP* 3.6 15.0 - - - +
151E LEU* 4.5 5.0 - - + +
154E ILE* 3.6 38.6 - - + -
177E ASN 3.7 2.7 - - - +
178E GLY* 3.8 16.4 - - - -
179E ASN 5.0 0.7 - - - -
180E ILE* 4.1 16.1 - - + +
78G ILE* 3.8 27.4 - - + -
81G CYS* 3.4 24.9 + - + +
99G LEU 3.8 0.7 - - - +
100G ALA* 3.2 2.6 - - - -
101G LEU* 2.5 48.8 + - + +
103G PHE* 3.7 27.1 - + - -
112G SER* 3.4 24.6 - - - -
113G ASP* 1.3 78.5 - - - +
115G GLU* 1.3 63.1 - - - +
116G MET 3.9 0.8 + - - -
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Residues in contact with GLU 115 (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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175E LEU 4.2 0.5 - - - +
176E GLY* 3.5 4.5 - - - -
177E ASN* 2.8 52.0 + - - +
178E GLY* 5.6 0.4 - - - -
179E ASN* 6.0 1.1 - - - +
78G ILE* 5.1 1.0 - - - +
91G ARG* 5.2 1.4 + - - -
98G THR* 4.1 14.8 + - - +
99G LEU 3.4 4.5 - - - -
100G ALA* 3.6 20.3 - - - +
113G ASP* 2.9 38.1 - - - +
114G TYR* 1.3 71.4 - - - +
116G MET* 1.3 61.4 + - - +
117G LYS* 3.9 0.3 + - - +
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Residues in contact with MET 116 (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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175E LEU 4.3 6.1 - - - +
70G VAL* 3.6 29.8 - - + -
71G ASN* 4.8 0.9 - - + +
74G SER* 4.3 8.7 - - - -
75G MET* 3.6 42.2 - - + -
78G ILE* 3.4 26.0 - - + -
98G THR* 3.4 3.9 - - - -
99G LEU* 2.7 70.3 + - + +
101G LEU* 4.3 8.5 - - + -
114G TYR 3.9 1.0 - - - -
115G GLU* 1.3 73.0 - - - +
117G LYS* 1.3 71.8 + - - +
118G LEU* 3.4 5.9 + - + +
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Residues in contact with LYS 117 (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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173E GLY 3.8 8.8 + - - -
174E GLU* 3.5 27.3 + - - +
175E LEU* 4.5 2.7 + - - +
176E GLY* 3.9 23.9 - - - +
177E ASN* 6.3 0.2 - - - +
70G VAL* 5.9 0.2 - - - -
71G ASN* 5.6 4.9 + - - +
97G ASP 4.2 4.5 - - - +
98G THR* 4.6 3.8 - - - +
115G GLU 3.9 0.8 + - - +
116G MET* 1.3 82.3 - - - +
118G LEU* 1.3 68.4 + - - +
119G MET* 4.9 8.4 - - + +
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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