Contacts of the helix formed by residues 111 - 130 (chain A) in PDB entry 5UC7
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 111 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110A ASP* 1.3 81.2 - - - +
112A GLY* 1.3 66.5 + - - +
113A SER* 3.8 5.0 + - - -
114A VAL* 3.3 25.5 + - - +
115A ALA 3.0 12.0 + - - -
274A LLP 4.1 11.4 + - - -
282A THR* 3.7 12.1 - - - -
283A LEU 4.8 1.1 - - - -
284A SER* 2.9 19.6 + - - +
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Residues in contact with GLY 112 (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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111A SER* 1.3 74.7 - - - +
113A SER* 1.3 62.3 + - - +
115A ALA* 3.2 1.7 + - - +
116A VAL* 3.0 19.4 + - - +
247A ILE* 3.3 33.6 - - - +
272A LEU 5.2 0.2 - - - -
273A GLY* 5.4 1.9 - - - -
274A LLP 3.4 24.3 + - - -
283A LEU 5.2 1.2 + - - -
284A SER* 4.1 7.3 - - - -
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Residues in contact with SER 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111A SER* 3.4 4.2 - - - -
112A GLY* 1.3 75.8 - - - +
114A VAL* 1.3 62.5 + - - +
116A VAL* 3.2 4.3 + - - +
117A GLU* 3.0 27.6 + - - +
145A HIS 4.3 10.1 - - - -
146A GLY* 3.4 5.6 - - - -
147A ASP* 3.2 24.5 + - - +
148A THR* 3.6 27.0 + - - -
151A ALA* 4.7 1.1 - - - +
274A LLP 2.8 25.1 + - - -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 3.9 20.6 - - + -
110A ASP* 4.7 9.4 - - + +
111A SER* 3.3 24.7 + - - +
112A GLY 3.2 0.6 - - - -
113A SER* 1.3 74.7 - - - +
115A ALA* 1.3 60.9 + - - +
117A GLU* 3.1 9.4 + - + +
118A VAL* 2.8 29.5 + - + +
148A THR* 5.5 7.9 - - + -
306A HIS* 3.8 25.6 - - + +
308A PRO* 4.6 6.7 - - + -
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Residues in contact with ALA 115 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A ALA* 4.9 2.9 - - + -
111A SER 3.0 6.5 + - - -
112A GLY* 3.4 10.1 - - - +
114A VAL* 1.3 77.9 - - - +
116A VAL* 1.3 55.9 + - - +
118A VAL* 3.4 4.6 + - - +
119A ALA 3.0 18.4 + - - -
247A ILE* 4.4 5.8 - - + -
271A CYS* 3.6 7.4 - - + -
272A LEU 4.3 7.0 - - - +
284A SER* 3.5 28.5 + - - +
285A ALA 4.4 3.6 - - - +
286A THR* 2.9 29.1 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112A GLY 3.0 12.4 + - - +
113A SER 3.6 7.0 - - - +
115A ALA* 1.3 72.6 - - - +
117A GLU* 1.3 68.0 + - - +
119A ALA* 3.0 3.2 + - - +
120A MET* 2.9 41.4 + - - +
145A HIS* 3.5 28.7 - - + +
151A ALA* 4.1 10.1 - - + -
209A ILE* 4.1 17.0 - - + -
245A ASP* 3.7 24.0 - - + +
247A ILE* 3.7 9.9 - - + -
271A CYS* 4.1 11.2 - - - -
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Residues in contact with GLU 117 (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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113A SER 3.0 17.7 + - - +
114A VAL* 3.5 11.0 - - + +
116A VAL* 1.3 75.8 - - - +
118A VAL* 1.3 58.7 + - - +
120A MET* 3.3 8.7 + - - +
121A LYS* 2.9 31.5 + - - +
148A THR* 2.6 29.8 + - + +
150A GLY* 2.9 34.5 + - - -
151A ALA 3.1 6.4 + - - +
306A HIS* 4.8 12.1 - - + -
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Residues in contact with VAL 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.9 21.8 - - + -
109A ALA* 4.9 1.1 - - + -
114A VAL* 2.8 28.8 + - + +
115A ALA* 3.5 7.0 - - - +
117A GLU* 1.3 72.3 - - - +
119A ALA* 1.3 58.3 + - - +
121A LYS* 3.2 4.7 + - - +
122A MET* 2.8 45.1 + - + +
286A THR* 4.1 9.9 - - - +
304A PHE* 3.5 24.9 - - + -
306A HIS* 3.7 36.6 - - + +
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Residues in contact with ALA 119 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A ALA 3.0 7.2 + - - +
116A VAL* 3.0 7.8 + - + +
118A VAL* 1.3 75.5 - - - +
120A MET* 1.3 63.5 + - + +
122A MET* 3.2 6.2 + - - +
123A ALA* 3.0 22.9 + - - +
243A ILE* 3.9 15.6 - - + +
269A ILE* 3.6 33.8 - - + +
271A CYS* 3.6 22.4 - - - -
286A THR* 4.1 3.4 - - + -
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Residues in contact with MET 120 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A VAL* 2.9 33.4 + - + +
117A GLU* 3.7 9.2 - - - +
119A ALA* 1.3 76.2 - - - +
121A LYS* 1.3 61.9 + - - +
123A ALA 3.3 1.0 + - - -
124A LEU* 3.0 30.5 + - + +
137A PHE* 3.6 49.0 - - + -
150A GLY* 3.4 38.6 - - - +
153A SER* 3.9 9.4 - - - +
154A VAL* 4.3 14.8 - - + -
209A ILE* 4.8 8.1 - - + -
243A ILE* 4.8 1.3 - - + -
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Residues in contact with LYS 121 (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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117A GLU 2.9 16.2 + - - +
118A VAL* 3.6 5.2 - - - +
120A MET* 1.3 75.3 - - - +
122A MET* 1.3 58.0 + - - +
124A LEU* 3.3 11.2 + - + +
125A GLN* 2.8 40.7 + - + +
304A PHE* 3.4 22.2 - - + -
305A MET* 2.8 33.6 + - + +
306A HIS* 2.9 26.1 + - - +
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Residues in contact with MET 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A PHE* 3.9 20.9 - - + -
118A VAL* 2.8 34.4 + - + +
119A ALA* 3.4 8.7 - - - +
121A LYS* 1.3 76.8 - - - +
123A ALA* 1.4 56.9 + - - +
125A GLN* 3.2 0.7 + - - -
126A TYR* 2.8 31.1 + - - +
241A LEU* 5.2 0.2 - - - -
269A ILE* 4.2 10.1 - - + -
286A THR* 3.8 17.7 - - + +
288A THR* 3.3 34.3 - - + -
292A VAL* 4.7 4.0 - - + -
296A ILE* 3.4 26.9 - - + +
304A PHE* 3.6 24.2 - - + -
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Residues in contact with ALA 123 (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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119A ALA 3.0 13.3 + - - +
120A MET 3.3 7.6 + - - +
122A MET* 1.4 76.1 - - - +
124A LEU* 1.3 62.2 + - - +
126A TYR* 3.3 1.9 + - - +
127A TRP* 3.2 29.6 + - - -
137A PHE* 3.9 20.0 - - + -
206A ALA* 4.3 5.8 - - + -
207A ALA* 4.0 12.3 - - + -
241A LEU* 3.8 25.1 - - + -
243A ILE* 4.4 2.9 - - + -
269A ILE* 4.4 1.7 - - + +
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Residues in contact with LEU 124 (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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120A MET* 3.0 24.0 + - + +
121A LYS* 3.3 10.9 + - - +
123A ALA* 1.3 76.0 - - - +
125A GLN* 1.3 64.4 + - - +
126A TYR 3.3 0.3 + - - -
127A TRP* 3.3 4.7 + - - +
128A GLN* 3.1 35.1 + - - +
134A ARG 3.4 26.6 - - - +
135A GLN* 3.7 21.8 - - + +
137A PHE* 4.1 22.4 - - + -
206A ALA* 4.4 3.1 - - + -
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Residues in contact with GLN 125 (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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121A LYS* 2.8 27.9 + - + +
122A MET* 4.6 0.2 - - - -
124A LEU* 1.3 73.0 - - + +
126A TYR* 1.3 61.8 + - - +
128A GLN* 3.2 21.5 + - - +
129A ALA* 3.0 25.6 + - - +
296A ILE* 3.7 26.5 + - + +
299A GLY* 5.5 2.1 - - - +
301A ALA* 3.5 15.2 - - - +
303A CYS 3.2 21.8 + - - -
304A PHE* 3.2 15.8 - - - +
305A MET* 3.1 36.1 + - - +
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Residues in contact with TYR 126 (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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122A MET 2.8 16.6 + - - +
123A ALA 3.4 7.2 - - - +
124A LEU 3.2 0.2 - - - -
125A GLN* 1.3 79.1 - - - +
127A TRP* 1.3 96.5 + + - +
129A ALA 3.3 0.9 + - - -
130A LYS* 3.3 45.2 + - + +
239A GLY 4.6 5.2 + - - -
241A LEU* 3.9 24.8 - - + +
291A GLN* 3.6 27.2 + - - -
292A VAL* 4.1 30.3 - - + -
295A THR* 3.4 48.4 - - + +
296A ILE* 3.4 9.3 - - + +
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Residues in contact with TRP 127 (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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123A ALA 3.2 21.9 + - - -
124A LEU 3.3 6.2 + - - +
126A TYR* 1.3 98.3 - + - +
128A GLN* 1.3 61.3 + - - +
130A LYS* 3.0 31.8 + - + +
132A GLU* 2.9 58.3 + - + +
134A ARG* 3.6 61.0 - - + +
206A ALA* 2.9 39.9 + - + +
238A GLU 5.1 1.6 - - - -
239A GLY* 3.3 32.5 - - - -
240A ILE* 4.3 5.2 - - - -
241A LEU* 4.5 1.6 - - - +
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Residues in contact with GLN 128 (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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124A LEU* 3.1 34.6 + - - +
125A GLN* 3.2 23.1 + - - +
127A TRP* 1.3 77.2 - - - +
129A ALA* 1.3 60.4 + - - +
131A GLY* 3.1 13.8 + - - +
132A GLU 3.9 7.8 + - - +
135A GLN* 6.0 3.4 - - - +
299A GLY* 5.2 2.8 - - - -
300A GLU* 4.4 15.2 - - - +
301A ALA* 5.8 2.8 - - - +
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Residues in contact with ALA 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A GLN 3.0 12.3 + - - +
126A TYR 3.6 9.6 - - - +
127A TRP 3.3 0.2 - - - -
128A GLN* 1.3 74.1 - - - +
130A LYS* 1.3 59.0 + - - +
131A GLY 3.3 1.6 + - - -
295A THR* 3.0 33.9 - - + +
296A ILE* 4.9 0.4 - - - -
298A ASN* 4.2 8.3 - - + +
299A GLY* 3.6 26.2 - - - +
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Residues in contact with LYS 130 (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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126A TYR* 3.3 50.9 + - + +
127A TRP* 3.0 36.6 + - + +
129A ALA* 1.3 78.3 - - - +
131A GLY* 1.3 61.4 + - - +
132A GLU* 3.3 13.0 + - + +
291A GLN* 5.3 4.8 - - - +
295A THR* 4.2 11.0 + - + +
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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