Contacts of the strand formed by residues 175 - 182 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1225A ASP* 2.4 44.5 + - - +
1227A HIS 3.7 15.3 + - - -
1228A PHE* 3.5 17.4 - - - +
1229A ARG* 4.4 12.6 - - + +
1340A SER* 4.5 3.4 - - - +
1341A GLU* 3.9 36.1 + - + +
170C LYS 3.7 0.3 - - - +
171C TYR* 3.3 12.1 - - - -
172C ALA 3.1 30.4 + - - +
173C ALA 4.3 2.0 - - - +
174C GLY* 1.3 82.6 - - - +
176C TYR* 1.3 71.7 + - - +
177C ASP* 3.9 0.7 + - - +
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Residues in contact with TYR 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228A PHE* 3.2 55.8 + - + +
1229A ARG 5.2 0.2 - - - -
1230A GLY* 4.6 11.7 - - - -
1231A LYS 4.1 15.8 + - - -
169C PHE* 3.7 31.2 - - + -
170C LYS 3.4 1.8 - - - +
171C TYR* 3.5 37.5 - + + -
175C LYS* 1.3 85.2 - - - +
177C ASP* 1.3 60.8 + - - +
178C ILE* 3.9 2.4 + - + -
329C ILE 4.6 4.0 + - - -
330C MET 4.9 0.3 + - - -
331C PRO* 3.5 43.0 - - + +
332C ASN* 6.1 0.2 - - - -
333C ILE* 4.5 19.7 - - + -
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Residues in contact with ASP 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169C PHE* 3.8 8.7 - - - +
170C LYS* 2.9 17.8 + - + +
175C LYS 3.9 1.1 + - - +
176C TYR* 1.3 71.8 - - - +
178C ILE* 1.3 64.9 + - - +
179C LYS* 2.8 42.4 + - - +
180C ASP* 2.9 38.8 + - + +
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Residues in contact with ILE 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1228A PHE* 3.7 40.8 - - + -
169C PHE* 3.7 9.4 - - + -
176C TYR* 3.9 2.7 + - + +
177C ASP* 1.3 75.9 + - - +
179C LYS* 1.3 71.2 + - + +
180C ASP 3.4 0.5 + - - -
181C VAL* 3.6 17.7 - - - +
333C ILE* 3.6 30.7 - - + -
335C GLN* 3.9 8.5 - - + +
369C ALA* 4.9 3.7 - - - +
1221C SER* 3.3 44.8 - - - +
1222C ALA* 4.1 5.6 - - + +
1225C ASP* 5.1 8.3 - - - +
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Residues in contact with LYS 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175A LYS* 4.3 20.8 - - - +
177C ASP* 2.8 19.3 + - - +
178C ILE* 1.3 80.8 - - + +
180C ASP* 1.3 56.7 + - - +
181C VAL* 3.6 7.3 + - - +
365C GLN* 4.6 5.9 + - - -
369C ALA* 4.9 8.1 - - - +
1222C ALA* 5.8 5.8 - - + -
1225C ASP* 4.8 6.6 + - - +
1341C GLU* 4.2 34.3 - - + +
1344C GLN* 6.3 1.1 - - - +
1345C PHE* 5.1 18.3 - - + -
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Residues in contact with ASP 180 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TYR* 2.7 26.0 + - - -
169C PHE* 3.5 2.9 - - - -
170C LYS* 3.1 43.6 + - + +
177C ASP* 2.9 27.7 + - - +
178C ILE 3.2 0.8 - - - -
179C LYS* 1.3 74.7 - - - +
181C VAL* 1.3 64.1 + - - +
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Residues in contact with VAL 181 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167C TYR* 4.0 1.5 + - - -
168C ALA 3.3 15.3 - - - +
169C PHE* 3.8 15.3 - - + -
178C ILE 3.6 20.9 - - - +
179C LYS 3.6 3.7 + - - +
180C ASP* 1.3 75.9 + - - +
182C GLY* 1.3 61.1 + - - +
183C VAL* 3.4 25.4 + - + +
339C PHE* 4.7 5.2 - - + -
365C GLN* 2.7 44.7 + - - +
368C ALA* 4.2 17.0 - - + -
369C ALA* 4.3 23.1 - - + +
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Residues in contact with GLY 182 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158C TRP* 4.7 0.3 - - - -
166C GLY* 3.5 5.2 - - - -
167C TYR* 2.9 69.4 + - - +
168C ALA 3.4 0.6 + - - -
181C VAL* 1.3 72.2 - - - +
183C VAL* 1.3 58.0 + - - +
184C ASP 3.6 1.3 - - - -
185C ASN* 3.5 16.4 + - - -
188C ALA* 4.1 0.3 - - - +
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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