Contacts of the strand formed by residues 155 - 163 (chain G) in PDB entry 3S4S
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 GLY 155 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133G PRO* 3.9 8.7 - - - -
153G ASP 3.3 3.0 + - - -
154G SER* 1.3 76.4 - - - +
156G THR* 1.3 62.7 + - - -
157G TRP* 4.1 0.8 + - - -
172G ILE 3.7 0.5 - - - +
173G ASP* 3.2 8.1 - - - +
174G ILE* 2.9 32.9 + - - +
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Residues in contact with THR 156 (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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131G ARG 4.3 1.2 - - - +
132G SER 4.6 0.2 - - - +
133G PRO* 4.0 17.3 - - - +
155G GLY* 1.3 73.7 - - - -
157G TRP* 1.3 69.7 - - - +
158G THR* 3.9 7.2 + - - +
171G LYS* 4.1 24.2 - - + +
172G ILE 3.4 6.3 - - - +
173G ASP* 2.8 22.8 + - - +
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Residues in contact with TRP 157 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G LEU* 5.9 4.7 - - + -
116G LEU* 5.1 8.5 - - + -
130G CYS* 4.0 17.5 - - + -
131G ARG 3.8 5.6 - - - -
132G SER* 3.2 43.5 - - - +
133G PRO* 3.4 14.5 - - + +
136G LYS* 4.2 7.6 - - + -
138G ILE* 4.8 14.6 - - + -
144G LEU* 6.0 1.3 - - + -
146G VAL* 4.7 21.5 - - + -
149G LEU* 4.7 10.5 - - + +
153G ASP* 3.1 38.2 + - + +
155G GLY 4.4 1.1 - - - -
156G THR* 1.3 74.9 - - - +
158G THR* 1.3 59.5 + - - +
159G CYS* 3.9 7.0 - - - -
170G PHE 3.7 1.0 - - - +
171G LYS* 3.3 8.7 - - - +
172G ILE* 2.8 43.1 + - + +
174G ILE* 3.1 34.6 - - + +
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Residues in contact with THR 158 (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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129G GLN 3.9 1.2 - - - +
130G CYS* 3.3 3.0 - - - -
131G ARG* 3.1 48.3 + - - +
156G THR* 4.0 6.4 + - - +
157G TRP* 1.3 73.9 - - - +
159G CYS* 1.3 61.1 + - - +
160G THR* 3.9 4.9 + - - +
169G GLU* 3.1 33.4 - - + +
170G PHE 3.5 2.5 - - - +
171G LYS* 3.2 21.4 + - - +
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Residues in contact with CYS 159 (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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100G LEU* 3.5 28.3 - - + -
116G LEU* 3.5 21.8 - - - -
128G VAL* 4.2 4.7 - - + -
129G GLN 3.5 4.0 - - - -
130G CYS* 2.0 44.4 - - - +
157G TRP* 3.9 6.7 - - - -
158G THR* 1.3 72.9 - - - +
160G THR* 1.3 60.0 + - - +
161G VAL* 4.2 1.7 + - + -
168G VAL 4.1 0.3 - - - +
169G GLU* 3.7 3.0 - - - +
170G PHE* 2.8 40.3 + - - +
172G ILE* 4.8 4.5 - - - -
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Residues in contact with THR 160 (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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127G SER 3.8 1.2 - - - +
128G VAL* 3.6 2.5 - - - -
129G GLN* 2.7 50.5 + - - +
158G THR* 4.7 4.9 + - - +
159G CYS* 1.3 76.6 + - - +
161G VAL* 1.3 65.7 + - - +
162G LEU* 4.1 1.0 + - + +
167G LYS* 3.4 43.1 - - + +
168G VAL 3.8 7.6 - - - +
169G GLU* 4.9 9.2 + - - +
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Residues in contact with VAL 161 (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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5G LEU* 6.1 0.2 - - - +
98G PHE* 4.4 14.8 - - + -
100G LEU* 5.1 2.9 - - + -
118G LEU* 3.7 45.5 - - + -
126G PRO* 4.1 15.0 - - + -
127G SER 3.6 4.5 - - - +
128G VAL* 3.9 9.9 - - + -
160G THR* 1.3 77.7 - - - +
162G LEU* 1.3 65.4 + - - +
163G GLN* 4.1 0.6 + - - +
166G LYS 3.7 0.5 - - - +
167G LYS* 3.5 6.1 - - - +
168G VAL* 3.0 44.8 + - + +
170G PHE* 4.2 17.9 - - + -
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Residues in contact with LEU 162 (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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125G SER 4.4 1.7 - - - +
126G PRO* 3.6 21.3 - - - +
127G SER* 3.2 27.7 + - - +
160G THR* 4.1 1.1 + - + +
161G VAL* 1.3 73.2 - - - +
163G GLN* 1.3 60.7 + - - +
165G GLN* 3.5 31.6 - - + +
166G LYS 3.1 22.7 - - - +
167G LYS* 3.3 30.1 - - + -
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Residues in contact with GLN 163 (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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5G LEU* 3.7 28.5 - - + +
96G LEU* 4.5 6.7 - - + +
98G PHE* 3.7 16.0 - - + -
123G GLY 4.9 1.8 + - - -
124G SER* 3.4 16.1 - - - +
125G SER* 2.8 45.9 + - - +
126G PRO* 3.2 11.1 - - + +
161G VAL* 4.1 1.7 + - + -
162G LEU* 1.3 74.3 - - - +
164G ASN* 1.3 92.9 + - - +
165G GLN 3.0 0.7 - - - -
166G LYS* 2.7 37.9 + - - +
168G VAL* 6.5 0.2 - - + -
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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