Contacts of the helix formed by residues 115 - 128 (chain B) in PDB entry 4WFH
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 115 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51A ARG* 4.2 3.6 - - - +
55A GLN* 4.5 3.8 - - - +
111B HIS* 5.2 3.8 - - - -
112B SER* 3.0 32.7 + - - +
114B TRP* 1.3 80.1 - - - +
116B LEU* 1.3 66.0 + - - +
117B GLY* 4.2 3.1 - - - -
118B SER* 2.9 28.9 + - - -
119B ALA* 2.9 16.8 + - - +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A VAL* 5.1 13.7 - - + -
47A ALA* 4.2 19.1 - - + -
48A LEU* 3.9 17.7 - - + +
51A ARG* 3.4 38.3 - - - +
115B ASP* 1.3 74.4 - - - +
117B GLY* 1.3 58.7 + - - +
119B ALA* 3.5 2.5 + - - +
120B PHE* 3.0 31.7 + - + +
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Residues in contact with GLY 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B ASP* 3.2 5.0 + - - -
116B LEU* 1.3 82.2 - - - +
118B SER* 1.3 55.4 + - - +
120B PHE* 3.4 9.4 - - - +
121B PHE* 3.1 25.8 + - - +
255B PRO 5.8 1.6 - - - -
258B GLN* 4.7 4.3 - - - +
259B PRO* 4.9 17.6 - - - +
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Residues in contact with SER 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B HIS* 5.7 1.6 + - - -
112B SER 4.1 3.6 + - - -
113B ALA* 3.1 27.5 - - - +
114B TRP* 5.6 0.2 - - - -
115B ASP* 2.9 24.1 + - - -
117B GLY* 1.3 73.7 - - - +
119B ALA* 1.3 59.7 + - - +
121B PHE* 3.4 9.6 - - - +
122B PHE* 2.8 28.4 + - - +
258B GLN* 3.5 18.7 + - - +
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Residues in contact with ALA 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A ALA* 3.5 31.1 - - + +
50A PHE* 4.8 1.5 - - + -
51A ARG* 4.3 2.7 - - + +
113B ALA 4.5 0.8 + - - -
114B TRP* 4.2 26.7 - - + +
115B ASP 2.9 16.2 + - - +
116B LEU* 3.8 2.0 - - - +
118B SER* 1.3 73.2 - - - +
120B PHE* 1.3 66.0 + - - +
122B PHE* 3.5 8.3 - - - +
123B SER* 3.0 27.4 + - - -
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Residues in contact with PHE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A LEU* 4.2 15.0 - - + -
43A LEU* 3.3 47.2 - - + +
44A VAL* 4.0 28.0 - - + -
47A ALA* 3.4 9.9 - - + +
116B LEU* 3.0 23.2 + - + +
117B GLY* 3.4 8.1 - - - +
119B ALA* 1.3 74.6 - - - +
121B PHE* 1.3 66.4 + - - +
123B SER* 3.1 7.7 + - - -
124B GLY* 3.0 18.2 + - - -
259B PRO* 4.1 31.9 - - + -
262B TRP* 4.9 17.7 - + + -
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Residues in contact with PHE 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLY 3.1 10.5 + - - +
118B SER* 3.4 14.1 - - - +
120B PHE* 1.3 85.1 - - + +
122B PHE* 1.3 65.7 + - - +
124B GLY* 3.0 12.3 + - - +
125B THR* 3.0 32.7 + - + +
132B TYR* 3.8 25.1 - + - -
134B ASN* 5.3 4.5 - - - -
231B PHE* 6.4 0.2 - + - -
245B VAL* 3.8 25.1 - - + -
246B ALA* 4.4 5.4 - - + -
258B GLN* 3.5 50.3 - - + +
259B PRO* 5.6 0.2 - - + -
261B VAL* 5.4 4.7 - - + -
262B TRP* 5.3 12.6 - + + -
265B ILE* 4.8 15.7 - - + -
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Residues in contact with PHE 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.9 23.6 - + - -
241A PHE* 3.7 35.9 - + - -
114B TRP* 3.7 27.8 - + + -
118B SER 2.8 19.9 + - - +
119B ALA* 3.5 7.6 - - - +
120B PHE 3.2 0.2 - - - -
121B PHE* 1.3 75.9 - - + +
123B SER* 1.3 63.1 + - - +
125B THR* 2.4 34.7 + - + -
126B ILE* 3.4 23.6 + - + +
133B GLY* 5.6 2.7 - - - -
135B VAL* 3.8 26.5 - - + -
137B LEU* 3.9 23.6 - - + -
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Residues in contact with SER 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.8 12.1 - - - -
46A GLY 3.6 1.0 - - - -
47A ALA 3.5 17.5 + - - -
50A PHE* 3.6 13.0 - - - -
119B ALA 3.0 15.0 + - - -
120B PHE 3.4 8.5 - - - -
122B PHE* 1.3 77.8 - - - +
124B GLY* 1.3 63.2 + - - +
126B ILE* 3.0 22.9 + - - +
127B ILE* 3.3 12.3 + - - +
149B TYR* 3.5 28.3 - - - -
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Residues in contact with GLY 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.6 15.4 - - - +
120B PHE* 3.0 9.1 + - - -
121B PHE 3.0 8.9 + - - -
123B SER* 1.3 76.9 - - - +
125B THR* 1.3 51.3 + - - +
126B ILE 3.1 1.0 + - - -
127B ILE* 3.5 2.7 + - - +
128B THR* 2.6 40.7 + - - +
262B TRP* 4.0 21.5 - - - -
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Residues in contact with THR 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A VAL* 4.4 0.2 - - - +
241A PHE* 4.4 6.1 - - - -
121B PHE* 3.0 40.3 + - + +
122B PHE* 2.4 35.6 + - + +
124B GLY* 1.3 75.7 - - - +
126B ILE* 1.3 59.5 + - - +
128B THR* 3.5 5.4 - - - -
129B THR* 3.7 0.5 - - - -
130B ILE* 3.1 13.5 + - + -
131B GLY* 2.8 39.4 + - - +
132B TYR* 3.8 21.3 - - + +
133B GLY 5.5 1.0 + - - +
134B ASN* 6.1 0.2 - - - +
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Residues in contact with ILE 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A PHE* 3.9 17.0 - - + -
239A VAL* 4.1 13.1 - - + +
241A PHE* 4.1 14.6 - - + -
122B PHE* 3.5 33.2 - - + +
123B SER* 3.0 7.1 + - - +
125B THR* 1.3 76.5 - - - +
127B ILE* 1.3 58.9 + - - +
128B THR 3.2 1.6 - - - -
129B THR* 2.7 25.8 + - - -
146B CYS* 3.7 26.2 - - - +
149B TYR* 4.1 12.3 - - + -
150B ALA* 3.5 35.9 - - + +
154B ILE* 3.8 8.7 - - - +
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Residues in contact with ILE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A VAL* 4.4 9.4 - - + -
42A TYR* 4.1 7.0 - - + -
43A LEU* 3.5 31.2 - - + -
123B SER 3.9 2.9 - - - +
124B GLY* 3.6 10.5 - - - +
126B ILE* 1.3 76.7 - - + +
128B THR* 1.3 63.4 + - + +
129B THR* 3.1 3.9 + - - +
149B TYR* 3.9 26.5 - - + +
153B GLY* 3.6 35.9 - - - +
154B ILE* 3.6 25.8 - - + +
156B LEU* 6.5 0.7 - - + -
157B PHE* 3.7 38.4 - - + -
262B TRP* 5.0 1.3 - - + -
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Residues in contact with THR 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B GLY 2.6 25.2 + - - +
125B THR* 3.4 5.4 + - - -
127B ILE* 1.3 76.7 - - + +
129B THR* 1.3 71.2 + - - +
130B ILE* 3.0 38.9 + - + +
157B PHE* 3.8 33.8 - - + -
238B THR* 4.0 9.4 - - - +
262B TRP* 4.2 13.9 - - + +
265B ILE* 4.7 2.0 - - + -
269B LEU* 4.0 13.8 - - + +
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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