Contacts of the strand formed by residues 154 - 165 (chain A) in PDB entry 4FO9
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 154 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A LEU* 3.2 30.3 + - + +
152A PRO 3.3 1.8 - - - +
153A PHE* 1.3 90.1 - - + +
155A ASP* 1.3 62.7 + - - +
156A VAL* 4.0 3.5 + - + +
208A GLN* 3.7 16.1 + - - -
210A GLN* 3.7 24.7 - - - +
260A PRO* 4.8 8.2 - - + +
262A ASN* 5.9 1.7 - - - +
296A VAL* 3.7 29.2 - - + -
297A ARG 3.3 3.8 - - - +
298A GLN* 3.6 45.6 + - + -
299A LEU* 4.4 2.2 - - - -
504A UNX 2.4 30.8 - - - -
506A UNX 4.2 0.2 - - - -
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Residues in contact with ASP 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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154A TYR* 1.3 75.0 - - - +
156A VAL* 1.3 63.5 + - - +
157A LEU* 3.5 3.9 + - + +
296A VAL* 3.2 6.0 - - - -
297A ARG* 2.9 37.1 + - + +
299A LEU* 3.7 14.2 - - - +
307A ARG* 2.9 43.6 + - - -
504A UNX 4.6 0.4 - - - -
516A UNX 3.1 26.1 - - - -
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Residues in contact with VAL 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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150A ASN* 5.7 4.5 - - - +
154A TYR* 4.0 5.6 + - + +
155A ASP* 1.3 72.9 - - - +
157A LEU* 1.3 62.9 + - - +
158A ASP* 3.8 23.3 - - - +
159A VAL* 4.8 4.9 - - + -
210A GLN* 5.8 0.7 - - - +
212A ARG* 6.3 1.3 - - - +
294A TYR* 4.0 22.7 - - + -
295A LEU 3.8 4.0 - - - +
296A VAL* 4.5 10.3 - - + -
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Residues in contact with LEU 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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155A ASP* 4.1 10.5 - - + +
156A VAL* 1.3 77.3 - - - +
158A ASP* 1.3 61.1 + - - +
190A GLU* 4.9 8.3 - - + -
207A VAL* 3.9 34.3 - - + -
295A LEU* 2.7 32.8 + - + +
296A VAL 4.3 5.8 - - - +
297A ARG* 4.2 15.9 - - + +
516A UNX 3.5 24.9 - - - -
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Residues in contact with ASP 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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156A VAL* 3.7 5.7 - - - +
157A LEU* 1.3 82.5 - - - +
159A VAL* 1.3 85.1 + - - +
160A LEU* 4.0 6.1 - - + +
187A GLN* 2.8 33.0 + - - +
294A TYR* 3.4 6.1 - - - +
295A LEU* 3.0 34.1 + - + +
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Residues in contact with VAL 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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156A VAL* 4.8 5.8 - - + -
158A ASP* 1.3 89.3 + - - +
160A LEU* 1.3 61.4 + - - +
161A ILE 3.7 6.1 - - - +
162A LYS* 3.7 43.3 - - + +
163A PRO* 4.9 2.9 - - + -
293A VAL 3.9 3.8 - - - +
294A TYR* 4.1 23.3 - - + -
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Residues in contact with LEU 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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158A ASP* 3.7 20.6 + - + +
159A VAL* 1.3 74.0 - - - +
161A ILE* 1.3 64.6 + - - +
180A ILE 5.3 0.2 - - - +
181A PHE* 4.0 35.5 - - + +
182A ALA 5.3 4.5 - - - +
183A LEU* 4.1 20.6 - - + -
187A GLN* 4.1 14.6 - - - +
209A VAL* 4.2 8.3 - - + -
293A VAL* 2.7 26.1 + - + +
294A TYR 4.0 18.6 - - - +
295A LEU* 4.1 15.0 - - + +
515A UNX 3.4 18.3 - - - -
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Residues in contact with ILE 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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159A VAL* 3.7 4.5 - - - +
160A LEU* 1.3 82.9 - - - +
162A LYS* 1.3 76.3 + - - +
164A THR* 3.9 6.3 - - - +
179A PHE* 3.8 33.7 - - + -
180A ILE 4.2 9.6 - - - +
181A PHE* 4.1 25.1 - - + -
277A ILE* 4.5 1.3 - - + -
291A MET* 3.7 18.8 - - + -
292A SER* 3.3 3.5 - - - -
293A VAL* 2.9 55.1 + - + +
502A UNX 3.6 11.4 - - - -
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Residues in contact with LYS 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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159A VAL* 3.7 17.4 - - + +
161A ILE* 1.3 80.6 - - - +
163A PRO* 1.3 67.6 - - + +
164A THR* 2.7 24.8 + - - +
291A MET 3.5 1.4 - - - +
502A UNX 3.1 15.3 - - - -
511A UNX 4.2 9.4 - - - -
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Residues in contact with PRO 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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145A GLN 3.9 6.5 - - - +
146A GLY 3.7 31.0 - - - +
147A GLN* 3.9 26.7 - - - +
159A VAL* 4.9 4.5 - - + -
162A LYS* 1.3 88.1 - - + +
164A THR* 1.3 60.8 + - - +
290A SER* 3.9 4.9 - - - +
291A MET 3.4 9.4 - - - +
292A SER* 3.7 13.9 - - - +
294A TYR* 4.2 5.8 - - + +
511A UNX 3.4 23.2 - - - -
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Residues in contact with THR 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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161A ILE* 3.9 6.9 - - - +
162A LYS* 2.7 23.3 + - - +
163A PRO* 1.3 75.5 + - - +
165A SER* 1.3 72.6 + - - +
166A LEU 3.5 0.3 + - - -
179A PHE* 3.8 28.5 - - + -
290A SER* 3.6 5.5 + - - -
291A MET* 3.0 34.9 + - - +
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Residues in contact with SER 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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164A THR* 1.3 84.2 - - - +
166A LEU* 1.3 63.5 + - - +
167A VAL* 3.3 23.8 + - - +
179A PHE* 5.3 1.4 - - - -
289A TYR 3.7 10.5 - - - -
290A SER* 4.3 2.9 - - - +
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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