Contacts of the strand formed by residues 184 - 193 (chain C) in PDB entry 4YHP
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 TYR 184 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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41C PRO* 6.0 2.1 - - - +
91C THR* 5.7 2.9 - - - +
118C THR* 4.5 14.3 + - + +
152C ASP* 2.9 24.1 + - - -
153C TYR* 2.8 50.3 + - + +
154C PHE* 3.8 24.4 - + - -
155C PRO* 4.2 2.0 - - + -
156C GLU* 3.8 46.0 - - + +
176C ALA* 4.2 8.1 - - + -
177C VAL 3.4 12.1 - - - -
178C LEU* 3.6 40.3 - - + +
179C GLN* 3.9 0.4 - - - -
183C LEU* 1.3 75.5 - - - +
185C SER* 1.3 61.1 + - - +
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Residues in contact with SER 185 (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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149C LEU* 4.2 7.7 - - - +
150C VAL 3.3 6.3 + - - -
151C LYS* 3.3 30.1 - - - +
153C TYR* 3.9 1.7 - - - -
175C PRO 4.5 0.5 - - - +
176C ALA* 3.4 1.3 - - - -
177C VAL* 3.0 38.0 + - - +
179C GLN* 3.7 25.4 + - - -
184C TYR* 1.3 79.0 - - - +
186C LEU* 1.3 61.9 + - - +
161D GLN* 5.4 2.0 - - - -
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Residues in contact with LEU 186 (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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149C LEU* 3.5 6.9 - - - +
150C VAL* 2.6 65.4 + - + +
153C TYR* 3.5 22.0 - - - +
156C GLU* 5.3 0.4 - - - +
158C VAL* 3.6 17.3 - - + +
160C VAL* 4.1 15.3 - - + -
173C THR* 4.1 10.1 - - + -
174C PHE* 3.5 21.5 - - - +
175C PRO 4.3 2.7 - - - +
176C ALA* 3.9 12.6 - - + +
185C SER* 1.3 76.1 + - - +
187C SER* 1.3 71.3 - - - +
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Residues in contact with SER 187 (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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132C LEU* 3.9 18.9 - - - +
148C CYS 3.2 7.0 - - - -
149C LEU* 3.6 19.4 - - - +
173C THR* 3.8 0.3 - - - -
174C PHE* 2.9 46.1 + - - +
186C LEU* 1.3 81.5 + - - +
188C SER* 1.3 61.3 + - - +
189C VAL* 4.9 2.5 - - - -
134D VAL* 4.4 9.8 - - - +
177D SER* 5.2 8.3 - - - -
179D THR* 5.1 2.9 + - - -
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Residues in contact with SER 188 (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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132C LEU* 4.8 0.2 - - - +
147C GLY* 3.0 4.2 - - - -
148C CYS* 2.8 39.6 + - - -
150C VAL* 5.7 0.2 - - - -
160C VAL* 3.5 28.2 - - - +
162C TRP* 3.1 24.5 + - - -
171C VAL* 4.2 0.9 - - - +
172C HIS 3.4 4.1 + - - -
173C THR* 2.7 27.7 + - - +
186C LEU* 4.4 0.6 - - - +
187C SER* 1.3 72.8 - - - +
189C VAL* 1.3 62.4 + - - +
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Residues in contact with VAL 189 (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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132C LEU* 4.2 20.4 - - + -
146C LEU 3.3 10.8 - - - +
162C TRP* 4.6 1.6 - - - -
171C VAL* 3.3 6.4 - - - +
172C HIS* 2.8 62.9 + - + +
174C PHE* 3.9 19.7 - - + -
187C SER* 4.9 2.2 - - - -
188C SER* 1.3 78.4 - - - +
190C VAL* 1.3 62.5 + - - +
191C THR* 6.5 0.4 - - + -
119D PHE* 5.0 3.4 - - + -
134D VAL* 5.9 1.8 - - + -
136D LEU* 3.9 37.0 - - + -
138D ASN* 4.8 0.7 - - - +
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Residues in contact with VAL 190 (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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144C ALA 3.8 0.3 - - - +
145C ALA* 3.5 2.2 - - - -
146C LEU* 2.8 60.3 + - + +
162C TRP* 4.2 18.4 - - + +
167C LEU* 4.0 12.8 - - + -
169C SER 3.9 10.8 - - - +
170C GLY 3.4 5.6 - - - +
171C VAL* 3.7 25.8 - - + -
189C VAL* 1.3 78.8 - - - +
191C THR* 1.3 75.4 + - - +
192C VAL* 3.9 14.3 + - + -
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Residues in contact with THR 191 (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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143C THR* 4.1 19.7 - - + -
144C ALA 3.2 5.6 - - - +
145C ALA* 4.1 18.8 - - + -
169C SER 4.2 7.3 - - - +
170C GLY* 3.4 18.4 + - - +
189C VAL* 6.5 0.4 - - + -
190C VAL* 1.3 81.1 - - - +
192C VAL* 1.3 64.8 + - - +
115D SER* 6.2 0.2 - - - -
117D PHE* 4.6 8.1 - - + -
136D LEU* 5.3 1.1 - - + -
138D ASN* 3.3 33.1 + - - +
139D ASN* 5.0 1.2 + - - -
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Residues in contact with VAL 192 (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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143C THR* 3.6 7.0 - - - -
144C ALA 2.7 40.5 + - - +
146C LEU* 4.0 9.6 - - + -
167C LEU* 4.6 5.6 - - + -
190C VAL* 3.9 22.0 - - + -
191C THR* 1.3 80.2 - - - +
193C PRO* 1.3 72.6 - - + +
197C LEU* 3.9 12.6 - - + -
202C TYR* 3.2 51.6 - - + +
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Residues in contact with PRO 193 (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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142C GLY 3.2 10.3 - - - +
143C THR* 5.7 0.2 - - + -
192C VAL* 1.3 90.5 - - + +
194C SER* 1.3 62.0 + - - +
195C SER* 3.9 17.7 - - - +
196C SER* 2.4 39.6 + - - +
197C LEU* 3.6 6.4 - - - +
202C TYR* 4.5 2.0 - - - +
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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