Contacts of the strand formed by residues 184 - 193 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A ASP 3.0 23.6 + - - -
153A TYR* 2.9 51.9 + + + +
154A PHE* 4.1 22.3 - + - -
155A PRO* 5.2 0.2 - - + -
156A GLU* 3.6 42.6 - - + +
176A ALA* 3.6 21.8 - - + -
177A VAL 3.4 7.6 - - - -
178A LEU* 3.5 36.4 - - + +
179A GLN* 3.4 0.3 + - - -
183A LEU* 1.3 73.9 - - - +
185A SER* 1.3 60.9 + - - +
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Residues in contact with SER 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.9 12.3 - - - +
150A VAL 3.3 13.2 + - - -
151A LYS* 3.6 16.3 - - - +
153A TYR* 4.1 1.6 - - - -
175A PRO 4.6 0.2 - - - +
176A ALA* 3.5 1.5 - - - -
177A VAL* 3.0 38.1 + - - +
179A GLN* 3.5 27.7 + - - -
184A TYR* 1.3 77.2 - - - +
186A LEU* 1.3 64.0 + - - +
179B THR* 6.2 0.2 - - - +
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Residues in contact with LEU 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149A LEU* 3.5 6.8 - - - +
150A VAL* 2.7 63.3 + - + +
153A TYR* 3.3 23.6 - - + +
156A GLU* 5.1 1.6 - - - +
158A VAL* 4.5 18.4 - - + +
160A VAL* 4.2 13.9 - - + -
173A THR* 4.3 10.1 - - + -
174A PHE* 3.6 22.2 - - - +
175A PRO 4.5 2.2 - - - +
176A ALA* 4.0 11.7 - - + +
185A SER* 1.3 75.4 + - - +
187A SER* 1.3 70.5 + - - +
188A SER 4.3 0.4 - - - +
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Residues in contact with SER 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 3.6 21.3 - - - +
148A CYS 3.3 7.1 + - - -
149A LEU* 3.3 22.2 - - - +
173A THR* 3.9 0.3 - - - -
174A PHE* 3.0 45.1 + - - +
186A LEU* 1.3 78.6 - - - +
188A SER* 1.3 60.7 + - - +
189A VAL* 4.5 4.3 - - - -
134B VAL* 4.2 9.3 - - - +
177B SER* 5.1 9.0 - - - -
179B THR* 5.1 2.3 + - - -
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLY* 3.0 3.3 - - - -
148A CYS* 2.8 36.5 + - - +
150A VAL* 5.8 0.2 - - - -
160A VAL* 3.6 25.4 - - - +
162A TRP* 2.9 26.0 + - - -
171A VAL* 4.2 1.7 - - - +
172A HIS 3.3 5.4 + - - -
173A THR* 2.9 26.6 + - - -
186A LEU* 4.3 1.2 - - - +
187A SER* 1.3 74.1 - - - +
189A VAL* 1.3 61.5 + - - +
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Residues in contact with VAL 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132A LEU* 4.0 22.4 - - + -
146A LEU 3.4 13.0 - - - +
147A GLY* 4.0 0.7 - - - -
162A TRP* 4.7 2.5 - - - -
171A VAL* 3.3 5.0 - - - +
172A HIS* 2.7 60.0 + - + +
174A PHE* 3.7 23.6 - - + -
187A SER* 4.5 3.8 - - - -
188A SER* 1.3 80.4 + - - +
190A VAL* 1.3 60.7 + - - +
191A THR* 6.3 0.4 - - + -
119B PHE* 4.8 5.2 - - + -
134B VAL* 5.8 2.2 - - + -
136B LEU* 3.8 32.8 - - + -
138B ASN* 5.2 0.2 - - - +
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Residues in contact with VAL 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A ALA 3.9 0.3 - - - +
145A ALA* 3.5 2.8 - - - +
146A LEU* 2.9 57.1 + - + +
162A TRP* 4.3 11.2 - - + -
167A LEU* 3.8 31.0 - - + -
169A SER 3.7 22.0 - - - +
170A GLY 3.4 5.8 - - - -
171A VAL* 3.9 13.0 - - + -
189A VAL* 1.3 78.3 - - - +
191A THR* 1.3 74.0 + - - +
192A VAL* 3.9 8.2 + - + -
202A TYR* 5.2 0.2 - - + -
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Residues in contact with THR 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.8 17.9 - - + -
144A ALA 3.2 10.1 - - - +
145A ALA* 4.2 13.2 - - + -
169A SER 4.5 2.1 - - - +
170A GLY* 3.4 22.3 + - - +
189A VAL* 6.3 0.2 - - + -
190A VAL* 1.3 83.1 - - - +
192A VAL* 1.3 64.2 + - - +
193A PRO* 5.0 0.2 - - - +
117B PHE* 4.4 7.2 - - + -
136B LEU* 5.1 2.7 - - + -
138B ASN* 3.8 35.3 + - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A THR* 3.6 5.7 - - - -
144A ALA 2.8 37.9 + - - +
146A LEU* 4.1 18.6 - - + -
167A LEU* 4.6 5.6 - - + -
190A VAL* 3.9 20.6 - - + -
191A THR* 1.3 80.2 - - - +
193A PRO* 1.3 77.2 - - + +
196A SER* 4.0 1.3 - - - +
197A LEU* 4.3 8.3 - - + -
202A TYR* 3.4 46.4 - - + +
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Residues in contact with PRO 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY 3.6 11.0 - - - +
143A THR* 4.6 1.1 - - - +
192A VAL* 1.3 95.1 - - + +
194A SER* 1.3 62.7 + - - +
195A SER* 4.0 15.5 - - - +
196A SER* 2.7 35.1 + - - +
197A LEU 4.1 0.9 + - - -
202A TYR* 4.8 1.6 - - - +
139F ASN* 5.1 7.2 - - - +
171F ASP* 5.4 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