Contacts of the strand formed by residues 154 - 165 (chain A) in PDB entry 5E8A
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 ASP 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLN* 3.3 9.4 - - - +
151A ARG* 2.9 57.0 + - + +
153A ASN* 1.3 82.7 + - - +
155A VAL* 1.3 62.6 + - - +
156A ALA 3.9 0.7 - - - +
176A LYS* 3.3 12.3 - - - +
177A LEU* 3.4 24.2 - - + +
178A ASP* 2.9 32.2 + - - +
179A ASN 4.6 1.0 + - - -
225A VAL* 5.5 2.0 - - + -
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Residues in contact with VAL 155 (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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148A ASP* 3.5 29.4 - - + +
149A PHE 3.6 6.7 - - - +
150A GLN* 3.9 20.9 - - - +
154A ASP* 1.3 75.1 - - - +
156A ALA* 1.3 63.2 + - - +
157A PHE 3.7 22.9 - - - +
158A HIS* 3.8 8.1 - - + -
175A THR* 3.3 6.6 - - - +
176A LYS* 2.9 61.3 + - + +
181A TRP* 4.5 4.9 - - + -
225A VAL* 5.1 0.2 - - - -
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Residues in contact with ALA 156 (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 PHE* 2.8 16.5 + - + +
150A GLN* 4.5 0.4 - - - +
151A ARG* 4.7 3.5 - - + +
154A ASP* 3.9 3.0 + - - +
155A VAL* 1.3 72.5 - - - +
157A PHE* 1.3 58.9 + - + +
175A THR* 2.8 20.7 + - - +
209A PHE* 5.1 4.5 - - + -
221A TYR* 3.9 5.9 - - - -
224A ARG* 5.2 0.9 + - - +
225A VAL* 3.8 29.1 + - + +
231A ILE* 3.6 37.9 - - + -
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Residues in contact with PHE 157 (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 LEU* 3.6 3.5 - - + +
148A ASP* 3.6 0.3 - - - -
149A PHE* 2.9 59.0 + + + -
155A VAL* 3.3 2.4 - - - -
156A ALA* 1.3 80.0 - - - +
158A HIS* 1.3 68.1 + - - +
159A PHE* 4.0 20.6 - + + -
173A CYS* 3.9 19.5 - - - -
174A ASN 3.7 2.7 - - - -
202A VAL* 4.8 2.9 - - + -
209A PHE* 3.6 45.5 - + + -
211A VAL* 4.0 23.8 - - + -
219A LEU* 4.5 1.6 - - + -
221A TYR* 3.5 39.9 - + + -
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Residues in contact with HIS 158 (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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146A ALA* 4.1 12.6 - - + -
147A LEU 3.3 5.3 + - - -
148A ASP* 2.7 28.1 + - - +
155A VAL* 3.8 2.9 - - + -
157A PHE* 1.3 75.0 - - - +
159A PHE* 1.3 59.6 + - - +
160A ASN* 3.3 23.9 - - + +
172A VAL 4.5 3.6 - - - -
173A CYS* 3.1 11.1 - - - +
174A ASN 2.9 36.3 + - - +
181A TRP* 3.5 30.7 - + + -
302A 5KS 2.7 55.8 + + - -
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Residues in contact with PHE 159 (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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145A ILE* 5.9 1.3 - - + -
146A ALA* 3.3 4.7 - - - -
147A LEU* 2.9 59.0 + - + +
157A PHE* 4.0 23.3 - + + -
158A HIS* 1.3 72.3 - - - +
160A ASN* 1.3 59.0 + - - +
161A PRO* 3.6 23.0 - - + +
171A ILE* 3.8 15.9 - - + -
172A VAL 3.9 1.8 - - - -
173A CYS* 4.0 16.2 - - - -
192A PHE* 4.1 20.0 - + - -
200A ILE* 4.4 11.7 - - + -
211A VAL* 4.0 21.8 - - + -
213A VAL* 4.9 0.7 - - + -
218A LEU* 4.0 17.0 - - + -
219A LEU* 4.0 14.4 - - + -
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Residues in contact with ASN 160 (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 ARG* 4.2 4.0 - - - +
145A ILE 2.9 17.5 + - - -
158A HIS* 3.3 26.7 - - + +
159A PHE* 1.3 72.8 - - - +
161A PRO* 1.3 69.5 + - - +
162A ARG* 2.8 35.2 + - - +
171A ILE* 4.3 1.3 - - - +
172A VAL* 2.8 37.4 + - + +
302A 5KS 3.2 35.1 + - - -
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Residues in contact with PRO 161 (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 ARG* 3.4 5.2 - - - -
145A ILE* 3.1 50.9 + - + +
159A PHE* 3.6 23.1 - - + +
160A ASN* 1.3 89.7 + - - +
162A ARG* 1.3 59.5 - - - +
163A PHE* 4.2 5.6 - - + -
170A VAL 3.7 6.7 - - - +
171A ILE* 4.1 7.2 - - + -
190A PHE* 4.0 16.8 - - + -
192A PHE* 3.6 32.8 - - + -
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Residues in contact with ARG 162 (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 ASN 3.7 5.6 - - - +
144A ARG* 4.7 3.4 - - + +
160A ASN* 2.8 24.0 + - - +
161A PRO* 1.3 77.1 - - - +
163A PHE* 1.3 62.1 + - - +
164A ASN 3.4 1.7 + - - +
165A GLU* 2.9 40.4 + - + +
168A ARG 4.0 0.7 - - - +
169A ARG* 3.4 5.0 - - - -
170A VAL* 2.8 42.9 + - + +
172A VAL* 3.6 21.5 - - - +
186A ARG* 3.5 3.2 - - - +
190A PHE* 3.5 3.5 - - - -
302A 5KS 2.9 76.6 + - - -
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Residues in contact with PHE 163 (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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138A VAL* 3.7 22.2 - - + -
142A ALA* 3.3 26.0 - - + +
143A ASN* 2.9 25.5 + - - +
144A ARG* 4.0 2.5 - - - -
145A ILE* 3.9 25.6 - - + -
161A PRO* 4.5 4.7 - - + -
162A ARG* 1.3 76.1 - - - +
164A ASN* 1.3 62.0 + - + +
167A ASN 5.6 0.3 - - - -
168A ARG 3.8 3.2 - - - +
169A ARG* 2.8 46.0 + - - +
190A PHE* 3.8 24.5 - + - -
192A PHE* 3.8 23.1 - - + -
194A SER* 3.8 31.0 - - - -
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Residues in contact with ASN 164 (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 ASN* 4.4 13.9 + - - +
162A ARG* 4.5 2.2 - - - +
163A PHE* 1.3 83.5 - - + +
165A GLU* 1.3 58.2 + - - +
166A ASN* 3.8 2.4 + - - -
167A ASN* 2.8 43.0 + - - +
168A ARG 3.5 3.8 - - - +
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Residues in contact with GLU 165 (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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162A ARG* 2.9 39.0 + - + +
164A ASN* 1.3 72.8 - - - +
166A ASN* 1.3 83.6 + - - +
168A ARG* 2.9 28.6 + - - +
170A VAL* 3.7 19.0 - - + +
186A ARG* 2.7 35.6 + - - -
302A 5KS 4.4 7.9 + - - -
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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