Contacts of the strand formed by residues 161 - 166 (chain D) in PDB entry 4JHN
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 LEU 161 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D ALA* 4.3 3.1 - - + -
154D ALA 3.6 11.4 - - - +
155D LEU* 4.2 7.6 - - + -
159D GLY 3.8 2.0 + - - -
160D ARG* 1.3 72.7 - - - +
162D PHE* 1.3 72.5 + - - +
163D MET* 4.1 14.8 - - + -
185D GLN* 3.3 10.8 - - - +
186D VAL* 2.8 43.4 + - + +
192D VAL* 4.2 14.1 - - + +
195D ILE* 3.5 52.5 - - + -
204D PHE* 3.6 28.3 - - + -
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Residues in contact with PHE 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135D PHE* 3.6 32.3 - + - -
136D PHE* 4.0 25.8 - + + -
140D HIS* 4.2 20.0 - + - -
142D ILE* 6.2 0.2 - - + -
153D ALA* 3.2 4.2 - - - +
154D ALA 2.8 43.0 + - - +
156D THR* 4.9 5.8 - - + -
160D ARG* 3.8 48.5 - - + -
161D LEU* 1.3 74.1 - - - +
163D MET* 1.3 62.7 + - - +
164D TRP* 3.7 4.8 - - + -
183D PRO* 4.3 4.3 - - + -
184D GLN 3.2 6.7 - - - +
185D GLN* 3.7 36.8 - - + -
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Residues in contact with MET 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D SER 3.2 7.2 - - - +
153D ALA* 4.0 8.5 - - + -
161D LEU* 4.1 16.6 - - + -
162D PHE* 1.3 81.0 - - - +
164D TRP* 1.3 64.7 + - - +
171D GLN 4.1 0.7 - - - +
172D ILE* 3.8 37.7 - - + +
174D LEU* 4.6 0.9 - - - +
180D VAL* 4.1 1.4 - - - +
184D GLN* 2.8 35.5 + - - +
186D VAL* 3.7 19.5 - - + +
195D ILE* 4.1 5.2 - - + -
197D CYS* 3.7 30.5 - - - -
202D SER* 3.9 21.5 - - - +
214D PHE* 3.9 17.3 - - - -
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Residues in contact with TRP 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 4.0 10.3 - - + -
108D VAL* 5.4 0.9 - - + -
117D GLY 3.5 7.4 - - - -
118D GLN 2.8 29.2 + - - -
119D LEU 3.5 1.6 - - - -
120D GLY* 3.3 29.2 - - - +
133D ILE* 3.9 20.2 - - + -
136D PHE* 3.7 34.5 - + - -
145D LEU* 5.4 1.3 - - + -
151D THR* 3.6 2.4 - - - -
152D SER* 2.9 47.1 + - - +
153D ALA 4.1 5.8 - - - -
154D ALA* 3.9 16.6 - - + -
162D PHE 3.7 16.6 - - - -
163D MET* 1.3 85.8 - - - +
165D GLY* 1.3 60.3 + - - +
172D ILE* 3.7 9.0 - - - +
180D VAL* 3.6 19.5 - - + +
182D VAL 3.8 11.9 - - - +
183D PRO* 3.7 17.0 - - + -
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Residues in contact with GLY 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU 3.3 19.5 - - - -
118D GLN* 3.9 12.1 - - - -
150D ASN 3.5 8.7 - - - -
164D TRP* 1.3 76.0 - - - +
166D ASP* 1.3 65.3 + - - -
172D ILE* 3.5 4.6 - - - +
179D ASN* 3.3 2.4 - - - -
180D VAL 2.8 33.9 + - - -
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Residues in contact with ASP 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116D GLU* 3.7 35.7 + - + +
149D SER 4.6 2.0 - - - +
150D ASN* 2.8 24.5 + - + +
151D THR* 3.5 7.7 - - + +
165D GLY* 1.3 72.0 - - - -
167D ASN* 1.3 58.4 + - - +
168D SER* 2.9 41.2 + - - -
171D GLN* 3.3 33.8 + - - +
172D ILE* 3.6 7.5 - - - +
178D SER 3.4 4.5 - - - +
179D ASN* 4.1 2.7 - - - -
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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