Contacts of the strand formed by residues 140 - 147 (chain A) in PDB entry 5FWP
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 ALA 140 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A PHE* 4.5 8.1 - - + -
136A ALA 3.1 18.0 + - - +
137A TYR* 3.3 24.9 - - - +
139A VAL* 1.3 80.2 - - + +
141A GLU* 1.3 60.9 + - - +
142A LYS 3.6 13.2 + - - +
143A VAL* 4.0 12.8 - - + -
183A LEU* 4.5 3.6 - - - -
184A HIS 2.9 20.4 - - - +
185A LEU* 4.0 1.8 - - + +
186A LYS* 3.7 4.3 - - - -
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Residues in contact with GLU 141 (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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82A ARG* 3.2 29.3 + - - -
137A TYR* 4.2 2.1 - - - -
140A ALA* 1.3 72.8 - - - +
142A LYS* 1.3 63.4 + - + +
160A SER* 3.6 21.8 - - - +
184A HIS* 2.5 16.2 + - + +
185A LEU 3.7 4.7 - - - +
186A LYS* 3.5 33.4 - - + +
187A GLU* 3.7 5.2 + - - +
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Residues in contact with LYS 142 (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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137A TYR* 3.8 6.3 - - - -
140A ALA* 3.2 1.3 - - - +
141A GLU* 1.3 85.5 - - + +
143A VAL* 1.3 73.2 + - - +
144A VAL* 4.3 6.9 - - - +
158A GLU* 2.7 44.3 + - - -
159A SER* 3.5 15.5 - - - +
160A SER* 4.2 8.3 - - - +
184A HIS* 2.8 54.2 + - + +
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Residues in contact with VAL 143 (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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133A PHE* 3.7 23.8 - - + -
136A ALA* 3.8 22.4 - - + -
137A TYR* 3.4 25.7 - - + +
140A ALA* 4.0 7.0 - - + -
142A LYS* 1.3 80.1 - - - +
144A VAL* 1.3 65.8 + - - +
145A VAL* 4.0 4.3 - - + -
157A TRP* 3.2 6.8 - - - -
159A SER 3.0 33.2 + - - +
181A VAL* 3.8 22.2 - - + -
182A ILE 3.2 7.6 - - - +
183A LEU* 4.0 10.3 - - + -
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Residues in contact with VAL 144 (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 LYS* 4.3 7.0 - - - -
143A VAL* 1.3 77.7 - - - +
145A VAL* 1.3 62.6 + - - +
146A ILE* 4.0 21.1 - - + -
156A ALA* 4.4 8.5 - - + -
157A TRP 3.2 15.7 - - - +
158A GLU* 4.0 24.5 - - + +
180A LYS 3.3 3.8 - - - +
181A VAL* 3.4 1.6 - - - -
182A ILE* 2.7 52.6 + - + +
184A HIS* 4.0 20.2 - - - +
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Residues in contact with VAL 145 (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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93A MET* 3.9 26.7 - - + -
98A LEU* 4.2 5.2 - - + +
102A LEU* 3.9 17.3 - - + -
133A PHE* 3.9 20.4 - - + -
143A VAL* 4.0 5.2 - - + -
144A VAL* 1.3 76.0 - - - +
146A ILE* 1.3 58.0 + - - +
147A THR* 3.7 1.8 + - - -
155A TYR 3.5 2.9 - - - +
157A TRP* 2.7 53.1 + - + +
179A THR* 3.1 23.3 - - + +
180A LYS 3.6 2.7 - - - -
181A VAL* 4.3 10.5 - - + -
1691A ATP 5.8 1.3 - - + +
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Residues in contact with ILE 146 (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 VAL* 4.0 9.0 - - + -
145A VAL* 1.3 71.0 - - - +
147A THR* 1.3 61.8 + - - +
154A GLN* 3.5 31.4 - - + +
155A TYR 3.2 10.3 - - - +
156A ALA* 3.8 20.4 - - + -
171A HIS* 5.7 6.3 - - + -
173A GLU* 4.3 10.5 - - + +
175A ILE* 3.7 13.9 - - + +
179A THR* 2.7 18.2 + - - -
180A LYS* 2.7 45.2 + - + +
182A ILE* 3.9 24.5 - - + -
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Residues in contact with THR 147 (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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92A GLY* 3.4 1.6 - - - -
93A MET* 2.9 38.9 + - + +
98A LEU* 3.7 38.4 - - + -
145A VAL* 4.5 1.1 - - - +
146A ILE* 1.3 76.0 - - - +
148A LYS* 1.3 63.6 + - - +
153A GLU 3.4 2.8 - - - +
154A GLN* 3.3 1.4 - - - -
155A TYR* 2.8 33.0 + - - -
175A ILE* 4.0 3.6 - - - -
178A GLY 2.6 22.8 + - - -
179A THR* 3.6 10.7 - - - -
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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