Contacts of the helix formed by residues 131 - 150 (chain B) in PDB entry 5FFO
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 131 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127B SER 2.9 5.7 - - - +
128B MET* 3.1 20.0 + - + +
130B ASP* 1.3 106.9 - - - +
132B LEU* 1.3 66.1 + - - +
133B ASN* 3.4 2.9 - - - -
134B THR* 3.3 20.3 + - - +
135B ILE* 3.3 17.5 + - + +
254B ASP* 2.7 40.1 - - + +
314B THR* 4.9 8.6 - - + +
336B LEU* 6.2 3.1 - - + -
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Residues in contact with LEU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 4.9 13.2 - - - -
124B LEU* 5.2 4.7 - - + -
128B MET* 2.8 17.8 + - + +
129B ASP* 3.7 13.2 + - - +
130B ASP 3.6 1.8 - - - -
131B ASP* 1.3 76.9 - - - +
133B ASN* 1.3 60.3 + - - +
135B ILE* 2.9 24.8 + - + +
136B LYS* 3.2 46.6 + - + +
213B GLN* 4.1 20.9 - - + +
214B LYS 5.6 0.2 - - - -
215B ILE* 4.4 26.5 - - + -
46D GLU* 5.4 8.3 - - + +
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Residues in contact with ASN 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B ASP 5.0 1.6 + - - +
130B ASP 3.8 16.5 - - - +
132B LEU* 1.3 78.1 + - - +
134B THR* 1.3 71.3 + - - +
136B LYS* 3.8 10.0 + - - +
137B GLU* 3.2 32.9 + - + +
338B LYS* 6.1 3.6 - - - +
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Residues in contact with THR 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ASP 4.9 1.2 + - - -
131B ASP* 3.5 16.4 + - - -
132B LEU 3.1 0.8 + - - -
133B ASN* 1.3 87.5 + - - +
135B ILE* 1.3 60.1 + - - +
137B GLU* 3.7 5.5 - - - +
138B LEU* 2.9 26.2 + - - +
336B LEU* 3.5 24.9 - - + -
337B GLN 3.0 30.8 + - - +
338B LYS* 4.5 13.6 - - - +
340B SER* 3.9 4.9 + - - -
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Residues in contact with ILE 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.1 39.3 + - + +
122B MET* 3.6 31.9 - - + -
128B MET* 4.1 17.5 - - + -
131B ASP* 3.3 16.6 - - + +
132B LEU* 2.9 9.9 + - + +
134B THR* 1.3 81.2 - - - +
136B LYS* 1.3 54.7 + - + +
138B LEU* 3.1 3.1 + - + +
139B GLY* 2.7 32.2 + - - -
210B VAL* 4.0 1.9 - - + +
252B VAL* 3.5 28.0 - - + -
336B LEU* 4.4 17.9 - - + -
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Residues in contact with LYS 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B MET* 5.8 0.2 - - + -
132B LEU* 3.2 44.4 + - + +
133B ASN* 4.3 7.4 - - - +
135B ILE* 1.3 75.5 - - + +
137B GLU* 1.3 58.3 + - + +
139B GLY* 3.9 0.2 - - - -
140B SER* 3.2 29.3 + - - -
210B VAL* 3.2 42.4 - - + +
211B LYS* 2.8 30.6 + - + +
213B GLN 3.7 12.2 + - - -
44D LEU 5.7 1.2 + - - -
45D PRO* 5.6 4.8 - - - +
46D GLU* 5.6 10.9 - - - +
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Residues in contact with GLU 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133B ASN* 3.2 22.5 + - + +
134B THR* 3.7 6.9 - - - +
136B LYS* 1.3 78.2 - - + +
138B LEU* 1.3 58.1 + - - +
140B SER* 4.0 6.6 + - - +
141B ARG* 3.1 27.0 + - - +
338B LYS 3.6 17.8 - - - +
339B ASP* 5.4 1.7 - - - +
340B SER* 3.5 8.0 + - - +
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Residues in contact with LEU 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 3.1 31.2 - - + +
134B THR 2.9 17.2 + - - +
135B ILE* 3.1 8.7 + - + +
137B GLU* 1.3 78.0 - - - +
139B GLY* 1.3 59.5 + - - +
141B ARG* 4.5 0.9 - - + -
142B LEU* 2.9 37.2 + - + +
250B VAL* 5.2 1.3 - - + -
252B VAL* 4.7 5.4 - - + -
336B LEU* 4.6 6.3 - - + -
340B SER* 3.3 32.1 - - - +
343B ILE* 3.7 31.9 - - + -
344B LEU* 4.1 20.4 - - + -
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Residues in contact with GLY 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B TYR* 4.3 5.4 + - - -
135B ILE 2.7 19.1 + - - -
136B LYS 3.5 1.3 + - - -
138B LEU* 1.3 72.7 - - - +
140B SER* 1.3 51.5 + - - +
142B LEU* 3.2 3.1 + - - -
143B SER* 2.8 35.3 + - - -
206B PHE* 3.4 30.0 - - - -
207B ASN* 3.8 1.1 - - - -
210B VAL* 4.9 7.6 - - - -
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Residues in contact with SER 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136B LYS 3.2 17.7 + - - -
137B GLU* 4.0 7.3 + - - -
139B GLY* 1.3 73.8 - - - +
141B ARG* 1.3 64.9 + - - +
143B SER* 3.1 18.2 + - - +
144B LYS* 3.6 6.2 + - - +
207B ASN* 3.4 27.6 + - - +
210B VAL* 6.0 0.4 - - - +
211B LYS* 6.0 2.9 - - - -
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Residues in contact with ARG 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
137B GLU 3.1 21.6 + - - +
138B LEU* 4.1 2.9 - - + +
139B GLY 3.2 0.6 - - - -
140B SER* 1.3 82.0 + - - +
142B LEU* 1.3 61.5 + - - +
144B LYS* 3.4 12.5 + - - +
145B GLU* 3.4 25.5 + - + +
339B ASP* 3.8 19.0 + - - +
340B SER* 3.8 12.1 - - - +
341B GLY* 3.3 32.7 - - - +
344B LEU* 3.6 20.9 - - + +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B LEU* 3.7 33.4 - - + -
120B TYR* 4.7 13.2 - - + -
138B LEU* 2.9 24.7 + - + +
139B GLY 3.7 4.0 - - - +
141B ARG* 1.3 71.5 - - - +
143B SER* 1.3 56.1 + - - +
144B LYS 3.0 10.8 + - - -
145B GLU* 4.8 1.6 - - - +
146B MET* 3.2 40.3 + - + +
155B LEU* 3.7 22.7 - - + -
206B PHE* 4.5 8.1 - - + -
250B VAL* 4.9 4.3 - - + -
343B ILE* 6.3 0.9 - - + -
344B LEU* 3.9 21.6 - - + +
347B ILE* 4.0 23.8 - - + -
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Residues in contact with SER 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLY 2.8 9.2 + - - -
140B SER 3.1 7.8 + - - +
142B LEU* 1.3 73.1 - - - +
144B LYS* 1.3 57.8 + - - +
146B MET* 5.0 1.6 - - - -
153B PHE* 5.0 5.6 - - - -
155B LEU* 4.6 7.5 - - - +
203B ALA* 3.2 37.5 + - - +
206B PHE* 3.9 10.0 - - - -
207B ASN* 3.2 31.3 + - - -
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Residues in contact with LYS 144 (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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140B SER 3.8 8.3 - - - +
141B ARG* 3.6 9.9 - - - +
142B LEU 3.0 1.4 + - - -
143B SER* 1.3 80.7 - - - +
145B GLU* 1.3 81.1 + - - +
146B MET 3.1 2.6 + - - -
147B SER* 3.5 18.3 + - - -
148B LYS* 4.2 31.6 + - - +
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Residues in contact with GLU 145 (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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141B ARG* 3.4 23.9 + - + +
142B LEU* 5.0 1.3 - - - +
144B LYS* 1.3 86.8 - - - +
146B MET* 1.3 64.6 + - + +
147B SER 3.3 0.2 - - - -
148B LYS* 3.4 39.9 + - - +
149B LEU* 4.3 3.1 + - - +
344B LEU* 4.0 22.9 - - + -
348B ILE* 5.3 17.0 - - + +
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Residues in contact with MET 146 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B VAL* 3.7 31.0 - - + -
118B LEU* 4.9 9.9 - - + -
142B LEU* 3.2 32.5 + - + +
143B SER 5.4 0.2 - - - -
144B LYS 3.1 1.7 - - - +
145B GLU* 1.3 75.2 - - + +
147B SER* 1.3 61.8 + - - +
148B LYS 3.1 6.1 + - - -
149B LEU* 4.0 1.9 + - - +
150B THR* 3.3 32.7 + - + +
153B PHE* 3.4 48.9 - - + +
347B ILE* 4.7 21.3 - - + -
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Residues in contact with SER 147 (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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143B SER 6.0 0.2 - - - -
144B LYS* 3.5 11.2 + - - -
145B GLU 3.3 1.0 - - - -
146B MET* 1.3 78.2 - - - +
148B LYS* 1.3 62.7 + - - +
150B THR 3.0 18.4 + - - +
151B SER* 5.0 2.3 - - - -
153B PHE* 4.7 12.7 - - - -
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Residues in contact with LYS 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LYS* 4.2 30.5 - - - +
145B GLU* 3.4 39.8 + - + +
146B MET 3.1 1.2 - - - -
147B SER* 1.3 81.7 - - - +
149B LEU* 1.3 65.2 + - + +
150B THR* 3.2 2.7 + - - -
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Residues in contact with LEU 149 (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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113B ASP* 5.2 3.8 - - - -
145B GLU 4.3 3.0 + - - +
146B MET 4.0 2.9 + - - +
148B LYS* 1.3 79.5 - - + +
150B THR* 1.3 62.7 + - + +
348B ILE* 4.0 31.9 - - + +
351B TYR* 3.5 48.0 + - + -
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Residues in contact with THR 150 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113B ASP* 4.1 6.7 + - - -
114B TYR 3.0 27.6 + - - +
116B VAL* 4.6 7.4 - - + -
146B MET* 3.3 27.2 - - + +
147B SER* 3.0 25.7 - - - +
148B LYS 3.2 2.7 + - - -
149B LEU* 1.3 81.9 - - + +
151B SER* 1.3 61.8 + - - +
152B ASN 3.3 14.5 + - - +
153B PHE* 4.2 16.3 - - + +
351B TYR* 3.8 8.5 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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