Contacts of the helix formed by residues 117 - 136 (chain B) in PDB entry 6UPR
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 117 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ASP 3.9 21.1 - - - -
115B GLU* 3.7 25.4 + - - -
116B SER* 1.3 79.0 - - - +
118B ARG* 1.3 87.9 + - + +
119B PRO* 3.5 0.4 - - - -
120B ILE* 3.0 16.7 + - + +
121B VAL* 2.9 40.1 + - + +
170B VAL* 4.6 11.4 - - + -
171B THR* 4.1 23.6 + - + +
174B LYS* 3.6 56.8 + - + -
175B LEU* 5.5 0.7 - - + -
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Residues in contact with ARG 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115B GLU* 2.6 44.8 + - + +
116B SER 3.3 0.4 - - - -
117B TYR* 1.3 105.6 + - + +
119B PRO* 1.3 65.8 - - + +
120B ILE 3.2 0.2 + - - -
121B VAL* 3.2 3.4 + - - +
122B ASP* 2.7 47.8 + - - +
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Residues in contact with PRO 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80B CYS* 5.7 3.1 - - + -
81B VAL* 3.2 38.1 - - + +
83B LEU* 3.3 23.2 - - + +
115B GLU 3.9 6.7 - - - +
116B SER* 3.4 14.1 - - - +
118B ARG* 1.3 94.2 - - + +
120B ILE* 1.3 58.9 + - - +
122B ASP* 3.8 10.7 - - + +
123B TYR* 3.2 16.5 + - - +
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Residues in contact with ILE 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 33.7 - - + -
50B VAL* 4.2 12.6 - - + -
81B VAL* 4.5 2.2 - - + -
83B LEU* 3.8 19.1 - - + -
104B ALA* 4.1 13.7 - - + -
107B PHE* 3.9 33.0 - - + -
116B SER 4.0 12.1 - - - +
117B TYR* 3.0 12.0 + - - +
119B PRO* 1.3 75.2 - - - +
121B VAL* 1.3 65.3 + - - +
123B TYR* 3.3 3.1 + - - +
124B ILE* 3.1 33.0 + - + +
171B THR* 4.4 5.8 - - + -
175B LEU* 4.1 13.2 - - + -
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Residues in contact with VAL 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B TYR* 2.9 37.0 + - + +
118B ARG* 3.9 5.8 - - - +
120B ILE* 1.3 73.2 - - - +
122B ASP* 1.3 60.5 + - - +
124B ILE* 4.4 4.9 - - - -
125B ASP* 2.7 43.7 + - - +
174B LYS* 4.1 11.4 - - + +
175B LEU* 3.7 22.9 - - + -
178B LYS* 3.7 28.0 - - + -
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Residues in contact with ASP 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ARG* 2.7 41.8 + - - +
119B PRO* 3.8 8.8 - - + +
121B VAL* 1.3 76.5 - - - +
123B TYR* 1.3 56.9 - - - +
125B ASP* 3.9 4.6 - - - +
126B ALA* 2.9 29.6 + - - +
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Residues in contact with TYR 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 5.9 0.7 - - + -
83B LEU* 3.8 26.7 - - + -
85B PRO* 3.6 27.4 - - + +
100B THR* 4.5 4.7 - - - +
102B VAL* 3.6 29.3 - - + +
119B PRO 3.2 17.0 + - - +
120B ILE 3.7 4.3 - - - +
121B VAL 3.2 0.4 - - - -
122B ASP* 1.3 75.2 - - - +
124B ILE* 1.3 68.3 + - + +
126B ALA* 3.1 10.1 + - + -
127B GLN* 3.0 54.2 + - + +
148B THR* 4.7 6.2 + - - -
150B ILE* 3.8 30.3 - - + -
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Residues in contact with ILE 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B LEU* 3.8 15.3 - - + -
120B ILE* 3.1 18.8 + - + +
121B VAL* 3.8 4.9 - - - +
123B TYR* 1.3 77.9 - - + +
125B ASP* 1.3 64.9 + - - +
127B GLN* 3.2 7.7 + - - +
128B PHE* 3.2 45.9 + - + -
149B ARG* 5.7 0.2 - - - -
150B ILE* 4.1 20.4 + - + +
175B LEU* 3.8 26.2 - - + -
178B LYS* 4.0 20.6 - - + +
179B VAL* 3.5 25.6 - - + -
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Residues in contact with ASP 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121B VAL* 2.7 32.6 + - - +
122B ASP* 4.1 4.7 - - - +
124B ILE* 1.3 73.8 - - - +
126B ALA* 1.3 57.6 + - - +
128B PHE* 3.4 9.5 + - - +
129B GLU* 2.9 29.5 + - - +
178B LYS* 2.8 36.6 + - - +
300B TYR* 3.6 22.5 + - + +
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Residues in contact with ALA 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ASP 2.9 20.1 + - - +
123B TYR* 3.1 8.4 + - + +
125B ASP* 1.3 78.0 - - - +
127B GLN* 1.3 67.7 + - - +
129B GLU* 3.3 7.6 + - - +
130B ASN* 3.0 36.1 + - - +
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Residues in contact with GLN 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123B TYR* 3.0 62.7 + - + +
124B ILE* 3.8 5.6 - - - +
125B ASP 3.2 0.4 - - - -
126B ALA* 1.3 84.1 - - - +
128B PHE* 1.3 65.5 + - - +
130B ASN* 3.5 11.1 + - - +
131B TYR* 3.1 24.1 + - - +
145B TYR* 4.5 0.2 + - - -
148B THR* 2.9 61.7 + - - +
149B ARG* 3.7 12.5 - - - +
150B ILE 4.9 1.8 - - - +
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Residues in contact with PHE 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124B ILE* 3.2 33.7 + - + -
125B ASP* 3.6 11.0 - - - +
127B GLN* 1.3 77.5 - - - +
129B GLU* 1.3 56.0 + - - +
131B TYR 3.4 1.0 + - - -
132B LEU* 2.9 29.5 + - - +
149B ARG* 3.7 35.0 - - + -
150B ILE 5.3 2.5 - - - -
178B LYS* 3.4 30.3 - - + -
292B THR* 4.5 7.9 - - + -
296B HIS* 4.1 20.0 - - + -
297B TYR* 3.6 28.5 - + + -
300B TYR* 3.4 40.8 - + + -
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Residues in contact with GLU 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125B ASP 2.9 14.1 + - - +
126B ALA* 3.5 9.6 - - - +
127B GLN 3.2 0.2 - - - -
128B PHE* 1.3 76.8 - - - +
130B ASN* 1.3 66.2 + - - +
132B LEU* 3.2 4.1 + - - +
133B GLN* 3.0 59.1 + - + +
300B TYR* 2.7 33.4 + - - +
304B LYS* 3.6 21.8 + - - +
308B MET* 4.6 5.3 - - - +
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Residues in contact with ASN 130 (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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126B ALA* 3.0 26.8 + - - +
127B GLN* 4.2 13.3 + - - +
129B GLU* 1.3 81.5 - - - +
131B TYR* 1.3 60.6 + - - +
133B GLN* 3.5 10.3 + - - +
134B GLU* 3.3 18.9 + - - +
145B TYR* 3.3 21.6 + - + +
148B THR* 5.1 2.2 + - - +
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Residues in contact with TYR 131 (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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127B GLN 3.1 18.2 + - - +
128B PHE 3.6 4.0 - - - +
130B ASN* 1.3 76.1 - - - +
132B LEU* 1.3 63.8 + - - +
134B GLU* 3.1 14.7 + - + +
135B GLU* 3.1 33.0 + - + +
142B LEU* 5.1 12.2 - - + +
145B TYR* 3.3 36.0 + + - +
147B ASP* 4.1 9.4 - - + -
149B ARG* 3.5 46.5 + - + -
293B HIS* 3.6 16.3 + + - -
297B TYR* 3.3 20.6 - + + -
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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
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128B PHE 2.9 17.8 + - - +
129B GLU* 3.2 6.7 + - - +
131B TYR* 1.3 72.4 - - - +
133B GLN* 1.3 65.8 + - + +
135B GLU* 3.2 11.4 + - + +
136B LEU* 3.0 33.2 + - + +
297B TYR* 3.2 22.6 + - + +
300B TYR* 4.4 4.7 - - + -
301B ARG* 3.9 22.4 - - + +
304B LYS* 3.6 35.2 - - + -
305B LEU* 3.9 24.5 - - + -
308B MET* 4.2 11.4 - - + -
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Residues in contact with GLN 133 (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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129B GLU* 3.0 47.7 + - + +
130B ASN* 3.7 12.1 - - - +
131B TYR 3.2 0.2 - - - -
132B LEU* 1.3 76.2 - - - +
134B GLU* 1.3 63.1 + - - +
136B LEU* 3.3 13.3 + - - +
137B LYS* 3.2 30.8 + - - +
308B MET* 4.0 19.2 - - - +
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Residues in contact with GLU 134 (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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130B ASN 3.3 9.8 + - - +
131B TYR* 3.1 13.3 + - + +
133B GLN* 1.3 78.6 - - - +
135B GLU* 1.3 61.3 + - - +
137B LYS* 3.3 42.4 + - - +
140B ARG* 3.2 21.2 - - - +
141B SER* 3.6 27.2 + - - +
142B LEU* 3.7 24.0 - - + -
145B TYR* 3.5 37.5 - - + -
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Residues in contact with GLU 135 (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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131B TYR* 3.1 29.2 + - + +
132B LEU* 3.2 13.2 + - + +
134B GLU* 1.3 77.5 - - - +
136B LEU* 1.3 63.3 + - + +
137B LYS 3.2 1.4 - - - +
140B ARG* 3.2 34.0 + - - +
142B LEU* 4.7 12.1 - - + -
293B HIS* 4.4 5.4 - - - -
297B TYR* 3.0 30.8 + - - -
298B GLU* 5.6 0.2 - - - +
301B ARG* 3.6 21.7 + - - -
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Residues in contact with LEU 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.0 36.0 + - + +
133B GLN* 3.7 13.9 - - - +
134B GLU 3.2 0.2 - - - -
135B GLU* 1.3 77.1 - - + +
137B LYS* 1.3 64.6 + - - +
138B ILE* 3.7 8.7 + - - +
305B LEU* 4.3 16.8 - - + -
308B MET* 3.9 32.3 - - + -
310B PHE* 4.5 18.4 - - + -
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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