Contacts of the helix formed by residues 139 - 155 (chain U) in PDB entry 6FF7
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 SER 139 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135U ASP* 5.1 4.7 - - - +
136U GLY 5.4 0.4 - - - -
137U GLU 4.0 1.8 + - - -
138U PHE* 1.3 76.7 - - - +
140U LEU* 1.3 65.9 + - - +
141U HIS* 3.2 9.2 - - - -
142U GLU* 3.1 13.5 + - - +
143U GLN* 3.0 20.7 + - - +
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Residues in contact with LEU 140 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135U ASP* 5.2 8.4 - - - +
138U PHE 3.9 0.2 + - - -
139U SER* 1.3 74.2 - - - +
141U HIS* 1.3 58.2 + - - +
143U GLN* 3.3 9.1 + - - +
144U THR* 2.9 26.2 + - - -
245U ASP* 4.3 26.5 - - + +
246U LYS* 5.2 2.0 - - - +
249U TYR* 4.7 9.5 - - + +
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Residues in contact with HIS 141 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139U SER* 3.2 6.3 - - - -
140U LEU* 1.3 78.9 - - - +
142U GLU* 1.3 56.7 + - - +
144U THR* 3.0 9.6 + - - -
145U VAL* 2.9 27.9 + - - +
245U ASP* 4.6 14.4 - - + +
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Residues in contact with GLU 142 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92U MET* 6.0 6.1 - - + -
138U PHE* 4.4 9.2 - - + -
139U SER* 3.1 26.4 + - - +
141U HIS* 1.3 79.0 - - - +
143U GLN* 1.3 56.6 + - - +
145U VAL* 3.4 10.2 - - - +
146U LEU* 3.2 22.9 + - - +
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Residues in contact with GLN 143 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129U ALA 5.1 5.8 - - - +
130U ALA* 4.9 14.4 - - - +
138U PHE* 5.1 9.2 - - + +
139U SER 3.0 15.7 + - - +
140U LEU* 3.8 7.6 - - - +
142U GLU* 1.3 73.8 - - - +
144U THR* 1.3 61.3 + - - +
146U LEU* 3.5 10.4 + - + +
147U LEU* 3.0 24.3 + - - +
249U TYR* 6.1 0.4 - - - -
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Residues in contact with THR 144 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140U LEU 2.9 13.1 + - - -
141U HIS* 3.3 13.2 - - - -
143U GLN* 1.3 76.2 - - - +
145U VAL* 1.3 59.0 + - - +
147U LEU* 3.1 9.4 + - - +
148U LEU* 2.9 29.5 + - - +
245U ASP 5.5 1.1 - - - -
248U HIS* 4.9 7.9 - - - -
249U TYR* 4.5 23.8 - - - +
252U ARG* 4.7 6.0 - - - +
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Residues in contact with VAL 145 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U CYS* 5.0 10.6 - - + +
96U CYS* 6.1 4.0 - - - +
99U ASN* 5.5 2.8 - - - +
141U HIS 2.9 11.6 + - - +
142U GLU* 3.4 13.5 - - - +
144U THR* 1.3 76.1 - - - +
146U LEU* 1.3 55.8 + - - +
148U LEU* 3.5 7.2 + - - +
149U PHE* 2.9 28.5 + - - +
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Residues in contact with LEU 146 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U CYS* 5.5 3.4 - - - -
126U ILE* 5.1 6.5 - - + +
129U ALA* 5.6 3.8 - - + -
130U ALA* 4.5 24.1 - - + +
142U GLU 3.2 14.1 + - - +
143U GLN* 3.7 12.3 - - - +
144U THR 3.1 0.2 - - - -
145U VAL* 1.3 76.3 - - - +
147U LEU* 1.3 59.8 + - - +
149U PHE* 3.3 7.7 + - - +
150U LEU* 2.9 31.2 + - - +
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Residues in contact with LEU 147 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130U ALA* 5.7 1.5 - - - +
143U GLN 3.0 15.1 + - - +
144U THR* 3.3 11.9 - - - +
146U LEU* 1.3 74.8 - - - +
148U LEU* 1.3 57.7 + - - +
150U LEU* 3.2 6.5 + - - +
151U ASP* 2.8 29.1 + - - +
249U TYR* 5.6 1.6 - - - +
252U ARG* 4.4 23.1 - - + +
253U PHE* 5.2 4.0 - - + +
256U LEU* 5.2 7.2 - - + +
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Residues in contact with LEU 148 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99U ASN* 5.5 9.6 - - + -
144U THR 2.9 12.5 + - - +
145U VAL* 3.7 10.3 - - - +
147U LEU* 1.3 75.1 - - - +
149U PHE* 1.3 63.9 + - - +
151U ASP* 3.1 10.5 + - - +
152U HIS* 3.0 21.7 + - - +
252U ARG* 5.1 7.9 - - + +
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Residues in contact with PHE 149 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95U CYS* 4.2 28.3 - - + +
98U VAL* 6.0 3.8 - - + -
99U ASN* 5.6 6.2 - - + +
145U VAL 2.9 17.8 + - - +
146U LEU* 3.6 7.0 - - - +
147U LEU 3.3 0.2 - - - -
148U LEU* 1.3 74.1 - - - +
150U LEU* 1.3 63.2 + - - +
152U HIS* 3.1 11.0 + - - +
153U CYS* 3.0 19.3 + - - +
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Residues in contact with LEU 150 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130U ALA* 6.3 2.5 - - + -
146U LEU 2.9 17.3 + - - +
147U LEU* 3.6 6.3 - - - +
149U PHE* 1.3 74.0 - - - +
151U ASP* 1.3 65.2 + - - +
153U CYS* 3.1 10.1 + - - +
154U PHE* 3.0 24.4 + - - +
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Residues in contact with ASP 151 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147U LEU 2.8 14.0 + - - +
148U LEU* 3.1 14.3 + - - +
150U LEU* 1.3 77.6 - - - +
152U HIS* 1.3 56.7 + - - +
154U PHE* 3.4 5.4 + - - +
155U ASN* 2.9 30.6 + - - +
252U ARG 5.8 1.1 - - - +
255U GLU* 5.8 2.5 - - + -
256U LEU* 4.8 21.9 - - + +
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Residues in contact with HIS 152 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98U VAL* 6.2 2.0 - - + +
99U ASN* 6.3 2.7 - - - -
102U PHE* 5.5 11.7 - - + -
148U LEU 3.0 11.8 + - - +
149U PHE* 3.1 12.1 + - - +
151U ASP* 1.3 77.2 - - - +
153U CYS* 1.3 61.3 + - - +
155U ASN* 3.3 8.0 + - - +
156U SER* 3.2 25.4 + - - -
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Residues in contact with CYS 153 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149U PHE 3.0 12.1 + - - +
150U LEU* 3.1 13.4 + - + +
152U HIS* 1.3 74.3 - - - +
154U PHE* 1.3 61.2 + - - +
156U SER* 2.8 30.4 + - - +
157U LEU* 3.7 2.4 + - - -
162U ILE* 4.7 13.2 - - + +
166U VAL* 5.6 9.4 - - + +
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Residues in contact with PHE 154 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150U LEU 3.0 15.4 + - - +
151U ASP* 3.9 6.1 - - - +
153U CYS* 1.3 76.4 - - - +
155U ASN* 1.3 57.2 + - - +
156U SER 3.3 3.1 + - - -
157U LEU* 4.1 12.6 + - - +
166U VAL* 5.7 6.5 - - - -
259U ASP* 6.0 4.5 - - + -
260U LEU* 5.8 9.6 - - + +
266U THR* 5.7 8.3 - - - -
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Residues in contact with ASN 155 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151U ASP 2.9 18.2 + - - +
152U HIS* 3.5 8.7 - - - +
153U CYS 3.1 0.2 - - - -
154U PHE* 1.3 76.2 - - - +
156U SER* 1.3 58.1 + - - +
157U LEU 3.8 1.1 - - - -
259U ASP* 5.7 7.9 - - + -
456U ASN* 5.3 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
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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