Contacts of the strand formed by residues 183 - 190 (chain L) in PDB entry 3SDI
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 183 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40L ASN* 3.1 23.6 + - - +
177L ILE 3.6 1.0 - - - +
178L VAL* 3.5 4.9 - - - -
179L THR* 2.9 32.0 + - - +
180L LYS 3.4 1.8 - - - -
182L ASP* 1.3 80.7 - - - +
184L VAL* 1.3 61.0 + - - -
185L ARG* 4.2 0.6 - - - +
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Residues in contact with VAL 184 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36L ASP* 3.7 37.0 - - + +
40L ASN* 4.0 17.9 - - - +
42L VAL* 4.1 20.6 - - + -
176L LEU* 4.2 18.6 - - + -
177L ILE 3.4 6.5 - - - +
178L VAL* 4.2 12.3 - - + -
182L ASP 4.4 0.4 + - - -
183L GLY* 1.3 75.8 - - - +
185L ARG* 1.3 63.0 + - - +
186L LYS* 4.4 5.5 + - + +
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Residues in contact with ARG 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L VAL* 4.3 13.3 - - - +
152L ILE* 4.1 8.5 - - - +
175L ILE 3.7 0.5 - - - +
176L LEU* 3.4 5.5 - - - +
177L ILE* 2.8 76.1 + - + +
179L THR* 5.0 10.3 + - - +
183L GLY 4.1 0.8 + - - +
184L VAL* 1.3 74.4 - - - +
186L LYS* 1.3 70.2 + - - +
187L GLU* 3.6 24.5 + - - +
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Residues in contact with LYS 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L TYR* 5.4 2.1 + - - -
174L GLU* 4.4 23.1 - - + -
175L ILE 3.5 2.0 - - - +
176L LEU* 3.6 31.6 - - + -
177L ILE* 4.8 0.7 - - - -
184L VAL* 4.4 4.9 + - + +
185L ARG* 1.3 80.7 - - - +
187L GLU* 1.3 69.3 + - - +
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Residues in contact with GLU 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ILE* 3.8 23.4 - - - +
173L LEU 3.7 0.3 - - - +
174L GLU* 3.4 6.4 - - - +
175L ILE* 2.8 41.7 + - + +
177L ILE* 4.4 8.1 - - + -
185L ARG* 3.6 25.5 + - - +
186L LYS* 1.3 80.4 - - - +
188L PHE* 1.3 61.3 + - - +
189L TYR* 2.6 39.8 + - + +
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Residues in contact with PHE 188 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18L THR* 4.2 2.2 - - + -
30L TYR* 3.9 36.1 - + + -
171L ASP 4.9 2.0 - - - -
172L GLY* 4.0 14.6 - - - -
173L LEU 3.2 37.7 - - - -
174L GLU* 4.5 9.4 - - + +
187L GLU* 1.3 74.8 - - - +
189L TYR* 1.3 80.0 + - - +
190L GLU* 4.4 28.0 - - + -
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Residues in contact with TYR 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L ILE* 4.5 4.4 - - + +
156L ARG* 3.6 59.4 + - + +
172L GLY* 3.5 0.9 - - - -
173L LEU* 2.8 51.1 + - + +
175L ILE* 3.9 22.0 - - + -
187L GLU* 2.6 37.4 + - + +
188L PHE* 1.3 91.9 - - - +
190L GLU* 1.3 68.6 + - - +
191L LEU* 5.2 2.0 - - + -
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Residues in contact with GLU 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L ASP 4.1 9.8 - - - +
172L GLY* 4.6 0.7 - - - -
188L PHE* 4.4 19.4 - - + -
189L TYR* 1.3 76.8 - - - +
191L LEU* 1.3 68.4 + - - +
193L ARG* 4.2 15.7 + - - -
152M ARG* 3.2 38.5 + - - -
198V GLU* 4.3 12.5 - - - +
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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