Contacts of the strand formed by residues 161 - 168 (chain D) in PDB entry 4E4E
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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62A ARG* 2.8 23.1 + - - -
124B MLY 6.0 3.8 - - - -
147B ASP* 5.8 0.2 - - - +
137D VAL* 4.0 17.3 - - + -
138D MLY 3.7 0.9 - - - -
139D ASN* 3.9 35.9 - - + +
147D ASP* 6.1 1.1 - - + -
149D VAL* 4.5 16.6 - - + -
157D VAL* 3.8 32.9 - - + +
158D THR 3.2 10.0 + - - +
159D GLY 3.2 1.4 - - - -
160D PRO* 1.3 81.2 - - + +
162D VAL* 1.3 61.3 - - - +
163D PRO* 3.6 3.3 - - - +
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Residues in contact with VAL 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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62A ARG* 4.4 2.5 - - - +
137D VAL* 3.0 6.3 - - - -
138D MLY 2.9 44.3 + - + +
140D LEU* 3.7 37.9 - - + -
159D GLY 4.9 3.4 - - - +
160D PRO 4.4 0.9 - - - +
161D LEU* 1.3 73.2 - - - +
163D PRO* 1.3 79.1 - - + +
164D LEU* 3.4 5.7 + - + +
201D ARG* 3.9 24.0 - - + +
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Residues in contact with PRO 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A ARG* 4.2 18.6 - - - +
83D LEU* 3.7 37.7 - - + -
135D PHE* 4.0 11.4 - - + -
136D ILE 3.8 4.5 - - - +
137D VAL* 4.3 2.2 - - + -
157D VAL* 3.7 23.1 - - + +
161D LEU 3.6 8.3 - - - +
162D VAL* 1.3 87.0 - - + +
164D LEU* 1.3 60.6 + - - +
165D VAL 5.2 1.3 - - - +
166D ALA* 5.7 0.2 - - + -
201D ARG* 3.4 24.2 - - - +
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Residues in contact with LEU 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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87D ASN* 4.2 1.2 - - - +
103D LEU* 4.3 8.7 - - + -
136D ILE* 2.6 26.4 + - + +
137D VAL* 3.7 3.4 - - - -
138D MLY 3.7 18.2 - - + +
146D LEU* 3.6 31.6 - - + -
162D VAL* 3.9 12.6 - - + +
163D PRO* 1.3 79.9 - - - +
165D VAL* 1.3 66.9 + - + +
198D ALA* 3.6 18.6 + - + +
201D ARG* 3.0 29.0 + - - +
202D PHE* 3.7 42.4 - - + +
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Residues in contact with VAL 165 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87D ASN* 3.7 14.6 - - + +
134D ALA 3.8 0.5 - - - +
135D PHE* 3.2 7.9 - - - +
136D ILE* 2.9 45.1 + - + +
163D PRO* 5.3 0.7 - - - -
164D LEU* 1.3 87.2 - - + +
166D ALA* 1.3 62.2 + - - +
167D ILE* 3.9 28.2 - - + +
190D TRP* 4.3 7.9 - - + -
193D VAL* 4.2 16.6 - - + -
195D TRP* 3.9 22.4 - - + -
198D ALA* 3.8 18.4 - - + -
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Residues in contact with ALA 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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80D ASN 4.6 0.2 - - - +
83D LEU* 4.1 19.1 - - + -
84D PHE* 3.1 12.5 - - - +
87D ASN* 2.8 33.3 + - - +
133D TRP* 4.1 13.0 - - + -
134D ALA 3.7 4.0 - - - -
135D PHE* 3.5 27.1 - - + -
163D PRO* 5.7 0.2 - - + -
164D LEU 4.4 0.2 - - - -
165D VAL* 1.3 73.7 - - - +
167D ILE* 1.3 63.8 + - - +
201D ARG* 4.4 0.6 - - - +
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Residues in contact with ILE 167 (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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84D PHE* 3.9 2.2 - - + -
87D ASN* 4.7 1.3 - - - +
88D LEU* 5.4 0.2 - - + -
121D THR* 4.9 3.1 - - + -
125D LEU* 3.6 32.6 - - + +
133D TRP* 3.3 8.4 - - - -
134D ALA* 2.9 35.2 + - + +
136D ILE* 6.4 0.2 - - + -
165D VAL* 3.9 21.5 - - + +
166D ALA* 1.3 82.6 - - - +
168D ASP* 1.3 71.4 + - - +
169D ALA 3.7 0.3 + - - -
185D TYR* 4.6 0.9 - - - +
186D PHE* 4.8 3.6 - - + -
189D ILE* 4.1 34.1 - - + -
190D TRP* 4.1 17.0 - - + -
193D VAL* 4.1 20.4 - - + -
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Residues in contact with ASP 168 (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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26D HIS* 3.0 11.3 + - - -
81D HIS* 3.9 0.3 + - - -
84D PHE* 3.6 21.6 - - + -
133D TRP* 3.5 29.2 - - + -
167D ILE* 1.3 76.1 - - - +
169D ALA* 1.3 67.6 + - - +
170D TRP* 3.1 24.9 + - - -
173D ALA* 3.6 12.5 - - + +
185D TYR* 2.9 29.1 + - - -
186D PHE* 4.3 0.2 - - - -
301D MN 2.2 34.2 + - - -
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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