Contacts of the strand formed by residues 177 - 184 (chain E) in PDB entry 2SGD
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 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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94E PHE* 3.8 29.2 - - + -
99E PRO* 4.6 0.4 - - + -
100E ASN 3.3 13.5 - - - +
101E ASN 3.9 12.1 - - - +
102E ASP* 4.6 3.4 - - + -
168E THR* 3.6 0.9 - - - -
169E VAL* 2.8 43.2 + - + +
171E TYR* 4.0 14.4 - - + -
176E VAL* 1.3 82.6 - - - +
178E TYR* 1.3 59.9 + - - +
180E MET* 3.1 38.8 - - + -
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Residues in contact with TYR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASN* 3.1 43.1 + - + +
101E ASN* 5.2 3.3 - - - +
167E ALA 3.8 4.3 - - - -
168E THR* 3.5 25.8 - - + +
176E VAL* 3.4 36.9 - - + +
177E VAL* 1.3 74.3 - - - +
179E GLY* 1.3 66.3 + - - +
180E MET* 3.4 11.5 + - - +
229E GLN* 5.5 1.2 - - - +
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Residues in contact with GLY 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E ASN* 3.7 39.2 + - - -
167E ALA 3.4 6.1 + - - -
168E THR* 4.8 0.8 + - - -
178E TYR* 1.3 75.2 - - - +
180E MET* 1.3 58.7 + - - +
230E PRO* 3.5 27.0 - - - +
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Residues in contact with MET 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100E ASN 5.5 0.2 - - - +
102E ASP* 4.2 4.7 - - + -
165E LEU 3.6 0.7 - - - -
166E ASN 3.2 7.9 + - - -
167E ALA* 2.7 48.6 + - + +
169E VAL* 4.2 10.3 - - + -
177E VAL* 3.1 35.4 - - + -
178E TYR 4.0 10.3 - - - +
179E GLY* 1.3 78.1 - - - +
181E ILE* 1.3 65.4 + - - +
214E SER* 3.4 30.1 - - - +
227E PHE* 4.3 4.9 - - + -
228E PHE* 3.3 32.8 - - - +
229E GLN* 3.3 26.5 - - + +
230E PRO* 4.7 0.2 - - - -
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Residues in contact with ILE 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA* 3.6 24.9 - - + +
162E VAL* 4.1 22.4 - - + -
164E ALA 3.8 4.5 - - - +
165E LEU* 4.4 6.5 - - + -
179E GLY 5.1 0.2 - - - +
180E MET* 1.3 73.9 - - - +
182E ARG* 1.4 70.8 + - - +
183E THR* 4.0 13.2 - - + -
199E LEU* 4.8 4.0 - - + -
210E ILE* 4.1 16.4 - - + +
226E THR 3.7 0.9 - - - +
227E PHE* 3.1 9.4 - - - -
228E PHE* 2.9 42.9 + - + +
230E PRO* 3.9 35.7 - - + -
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Residues in contact with ARG 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162E VAL* 3.4 4.0 - - - +
163E THR* 2.9 39.9 + - - +
164E ALA* 2.9 30.8 + - + +
167E ALA* 4.3 7.2 - - + -
180E MET 3.7 1.6 + - - -
181E ILE* 1.4 70.4 - - - +
183E THR* 1.3 71.9 + - - +
225E THR* 4.0 25.9 + - + +
226E THR 4.0 2.5 - - - -
227E PHE* 3.8 31.4 - - + -
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Residues in contact with THR 183 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E VAL* 4.3 13.9 - - + -
161E SER 3.2 16.8 - - - +
162E VAL* 4.2 4.5 - - - -
163E THR* 3.8 9.4 - - - -
181E ILE* 4.0 11.4 - - + -
182E ARG* 1.3 82.3 + - - +
184E ASN* 1.3 58.7 + - - +
190E VAL* 3.0 19.3 + - - +
199E LEU* 4.5 0.9 - - + -
225E THR* 3.7 10.6 + - - +
226E THR 2.9 32.8 + - - -
228E PHE* 3.4 31.1 - - + -
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Residues in contact with ASN 184 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159E SER 5.0 1.4 - - - +
160E GLY* 3.4 7.3 - - - -
161E SER* 2.6 44.0 + - - +
163E THR* 3.9 14.2 - - + +
183E THR* 1.3 72.0 - - - +
190E VAL* 1.3 61.9 + - - +
191E CYS 3.8 1.0 + - - -
224E GLY 3.5 16.0 + - - +
225E THR* 4.9 1.6 - - - +
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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