Contacts of the strand formed by residues 175 - 182 (chain E) in PDB entry 5TJ4
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 175 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171E TYR* 3.4 12.6 - - - -
172E ALA 3.2 22.4 + - - +
173E ALA* 4.7 4.9 - - + +
174E GLY* 1.3 79.6 - - - +
176E TYR* 1.3 73.1 + - - +
177E ASP* 3.8 2.1 + - - +
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Residues in contact with TYR 176 (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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169E PHE* 3.7 32.3 - - + -
170E LYS 3.4 3.6 - - - +
171E TYR* 3.6 43.3 - + + -
175E LYS* 1.3 90.4 + - - +
177E ASP* 1.3 60.7 + - - +
178E ILE* 3.8 8.4 + - + +
329E ILE* 4.7 7.8 + - - +
331E PRO* 3.5 43.5 - - + +
332E ASN* 5.5 1.3 - - - -
333E ILE* 4.4 31.0 - - + -
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Residues in contact with ASP 177 (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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169E PHE* 3.8 8.7 - - - +
170E LYS* 3.0 17.9 + - + +
175E LYS* 3.8 1.5 + - - +
176E TYR* 1.3 71.3 - - - +
178E ILE* 1.3 63.0 + - - +
179E LYS* 2.8 37.1 + - - +
180E ASP* 2.9 39.3 + - + +
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Residues in contact with ILE 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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169E PHE* 3.7 19.3 - - + -
176E TYR* 3.8 10.3 + - + +
177E ASP* 1.3 75.6 + - - +
179E LYS* 1.3 64.2 + - + +
180E ASP 3.4 0.7 + - - -
181E VAL* 3.7 6.8 - - - +
333E ILE* 3.6 31.2 - - + -
335E GLN* 3.9 17.5 - - + +
369E ALA* 4.6 4.4 - - - +
1221E SER* 3.3 43.1 - - - +
1222E ALA* 4.1 7.2 - - + +
1225E ASP* 5.3 11.2 - - + +
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Residues in contact with LYS 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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177E ASP* 2.8 11.0 + - - +
178E ILE* 1.3 81.6 - - + +
180E ASP* 1.3 57.5 + - - +
181E VAL* 3.6 7.8 + - - +
365E GLN* 5.7 0.9 + - - -
369E ALA* 4.5 3.1 - - - +
1222E ALA* 6.1 2.5 - - + -
1341E GLU* 3.3 40.9 + - + +
1344E GLN* 4.8 12.7 + - - +
1345E PHE* 4.3 35.2 - - + -
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Residues in contact with ASP 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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167E TYR* 2.8 26.4 + - - -
169E PHE* 3.5 2.9 - - - -
170E LYS* 3.1 50.0 + - + +
177E ASP* 2.9 26.5 + - - +
178E ILE 3.2 1.2 - - - -
179E LYS* 1.3 74.3 - - - +
181E VAL* 1.3 63.9 + - - +
365E GLN* 5.3 1.7 + - - -
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Residues in contact with VAL 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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167E TYR* 4.1 1.3 + - - -
168E ALA 3.2 15.0 - - - +
169E PHE* 3.8 15.9 - - + -
178E ILE 3.7 17.5 - - - +
179E LYS 3.6 3.6 + - - +
180E ASP* 1.3 78.2 + - - +
182E GLY* 1.3 59.3 + - - +
183E VAL* 4.1 26.9 - - + +
339E PHE* 4.7 6.1 - - + -
365E GLN* 2.8 44.6 + - + +
368E ALA* 4.2 14.6 - - + -
369E ALA* 4.2 25.1 - - + +
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Residues in contact with GLY 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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158E TRP* 4.7 0.2 - - - -
166E GLY* 3.5 5.5 - - - -
167E TYR* 2.9 68.9 + - - +
168E ALA 3.4 2.6 + - - -
181E VAL* 1.3 69.6 - - - +
183E VAL* 1.3 59.3 + - - +
184E ASP 3.5 2.2 - - - -
185E ASN* 3.5 14.9 + - - -
365E GLN* 5.1 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