Contacts of the helix formed by residues 124 - 138 (chain A) in PDB entry 3U0V
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 124 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A GLY* 4.6 3.6 - - - -
30A SER 5.3 1.6 - - - -
80A ARG* 5.5 1.8 - - - -
123A PHE* 1.3 82.4 - - - +
125A MET* 1.4 61.3 + - - -
127A GLY 2.9 10.9 + - - -
128A CYS* 3.2 6.1 + - - +
147A LEU 2.5 15.6 + - - -
148A SER 3.3 14.5 + - - -
149A SER* 2.8 22.3 + - - -
182A VAL* 4.0 8.3 - - - +
211A HIS* 3.0 38.8 + - - -
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Residues in contact with MET 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A GLY* 4.2 1.3 - - - -
30A SER* 3.9 25.4 - - - +
66A TYR* 3.4 33.0 - - + +
76A VAL* 3.7 13.0 - - + -
77A TRP* 3.3 35.0 - - + -
78A PHE* 3.3 49.6 - - + +
80A ARG* 4.4 13.9 - - + +
123A PHE 3.1 0.8 + - - -
124A SER* 1.4 78.6 + - - +
126A GLY* 1.3 62.4 + - - +
128A CYS* 3.4 9.9 + - - +
129A MET* 3.1 19.1 + - - +
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Residues in contact with GLY 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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27A LEU* 3.4 27.1 - - - +
28A HIS 3.3 18.4 + - - -
77A TRP* 3.8 5.8 - - - -
122A GLY* 3.6 5.8 - - - -
123A PHE 2.9 9.2 + - - -
125A MET* 1.3 80.0 - - - +
127A GLY* 1.4 56.6 + - - +
129A MET* 4.3 0.7 - - - -
130A ALA* 2.9 24.8 + - - +
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Residues in contact with GLY 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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122A GLY 3.2 28.4 - - - -
124A SER 2.9 6.9 + - - -
126A GLY* 1.4 73.9 - - - +
128A CYS* 1.3 58.7 + - - -
130A ALA* 3.2 2.8 + - - +
131A MET* 2.9 38.7 + - - +
146A ALA* 4.1 7.0 - - - +
149A SER* 3.3 14.8 - - - -
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Residues in contact with CYS 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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78A PHE* 3.4 28.0 - - + -
80A ARG* 4.1 11.7 - - - +
89A GLU* 5.8 0.9 - - - -
94A ILE* 5.0 2.9 - - - -
124A SER 3.2 8.8 + - - +
125A MET 3.5 9.0 - - - +
127A GLY* 1.3 71.1 - - - +
129A MET* 1.3 65.2 + - - +
131A MET* 3.1 14.3 + - - +
132A HIS* 3.0 44.4 + - - -
149A SER* 3.7 5.0 + - - -
150A PHE 3.8 21.3 - - - +
151A LEU* 4.1 8.5 - - - -
152A ASN* 5.2 3.6 - - - -
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Residues in contact with MET 129 (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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27A LEU* 3.8 7.9 - - + -
77A TRP* 3.9 12.3 - - + -
78A PHE* 3.8 25.3 - - + -
94A ILE* 3.8 16.2 - - + +
97A MET* 3.7 23.8 - - - +
98A CYS* 3.6 39.9 - - - +
101A LEU* 3.5 25.4 - - + -
125A MET 3.1 16.3 + - - +
126A GLY* 3.7 6.1 - - - +
127A GLY 3.3 0.2 - - - -
128A CYS* 1.3 74.8 - - - +
130A ALA* 1.3 64.4 + - - +
132A HIS* 3.1 6.9 + - + +
133A LEU* 2.9 27.4 + - + +
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Residues in contact with ALA 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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27A LEU* 3.9 5.5 - - + +
120A ILE* 4.0 17.7 - - + +
121A GLY* 3.5 36.8 - - - +
122A GLY 4.1 0.4 - - - +
126A GLY 2.9 19.2 + - - +
127A GLY* 3.5 5.4 - - - +
128A CYS 3.2 0.2 - - - -
129A MET* 1.3 76.6 - - - +
131A MET* 1.3 57.5 + - - +
133A LEU* 3.3 4.2 + - - +
134A ALA* 2.9 32.4 + - - +
144A VAL* 3.9 6.9 - - + +
145A PHE 4.2 0.4 - - - +
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Residues in contact with MET 131 (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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127A GLY 2.9 22.9 + - - +
128A CYS* 3.1 17.2 + - - +
130A ALA* 1.3 76.3 - - - +
132A HIS* 1.4 57.2 + - - +
135A TYR* 2.9 48.4 + - + +
144A VAL* 4.2 14.1 - - + -
146A ALA* 4.1 11.7 - - + -
149A SER* 4.1 13.0 - - - -
150A PHE* 4.1 11.7 - - - +
151A LEU* 3.9 28.7 - - + -
157A VAL* 3.9 3.5 - - - +
171A LEU* 4.3 13.5 - - + -
173A GLN* 5.3 1.6 - - - +
190A THR* 4.3 8.1 - - + -
194A LEU* 4.0 25.4 - - - -
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Residues in contact with HIS 132 (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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78A PHE* 5.9 0.2 - + - -
89A GLU* 3.1 38.6 + - - -
91A LEU* 4.5 0.4 - - + -
94A ILE* 3.5 32.6 - - + +
98A CYS* 4.2 4.0 - - - -
128A CYS* 3.0 33.5 + - - -
129A MET* 3.6 8.3 - - + +
131A MET* 1.4 75.8 - - - +
133A LEU* 1.3 64.5 + - - +
136A ARG* 3.0 58.9 + - - +
137A ASN* 3.2 4.5 + - - -
151A LEU* 3.8 11.2 - - + +
155A SER* 3.5 13.2 + - - -
157A VAL* 3.7 14.1 - - + -
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Residues in contact with LEU 133 (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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25A ILE* 6.2 1.1 - - + -
27A LEU* 5.2 1.8 - - + -
98A CYS* 3.7 21.7 - - - +
101A LEU* 3.4 35.2 - - + -
102A THR* 3.6 16.4 - - - +
105A ILE* 3.8 22.2 - - + -
120A ILE* 4.4 20.4 - - + -
129A MET* 2.9 17.8 + - + +
130A ALA* 3.8 3.8 - - - +
132A HIS* 1.3 78.2 - - - +
134A ALA* 1.4 55.3 + - - +
137A ASN* 3.1 17.3 + - - +
138A HIS* 3.1 46.1 + - + +
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Residues in contact with ALA 134 (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 ILE* 5.1 5.8 - - + +
130A ALA 2.9 15.0 + - - +
131A MET 4.2 1.3 - - - +
133A LEU* 1.4 75.6 - - - +
135A TYR* 1.3 64.7 + - + +
138A HIS* 3.1 33.9 + - - +
139A GLN* 3.2 6.1 + - - -
141A VAL* 4.0 12.8 - - + -
144A VAL* 3.2 35.9 - - + -
169A PRO* 4.6 1.8 - - + -
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Residues in contact with TYR 135 (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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131A MET* 2.9 43.2 + - + +
134A ALA* 1.3 76.7 - - + +
136A ARG* 1.3 60.8 + - - +
139A GLN* 2.9 26.8 + - - -
144A VAL* 3.9 21.7 - - + +
157A VAL* 3.9 19.7 - - + -
160A ALA* 3.9 9.2 - - - +
161A LEU* 3.8 27.7 - - + +
168A LEU* 4.2 2.9 - - + -
169A PRO* 2.8 50.2 + - + -
170A GLU 3.7 0.9 - - - -
171A LEU* 3.4 26.2 + - + +
194A LEU* 4.8 11.4 - - + -
199A VAL* 3.4 19.2 - - + +
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Residues in contact with ARG 136 (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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91A LEU* 3.4 19.6 - - - +
94A ILE* 3.7 6.3 - - - +
95A ASP* 2.8 35.3 + - - -
98A CYS* 4.3 6.6 - - - -
132A HIS* 3.0 50.8 + - - +
134A ALA 3.3 0.2 - - - -
135A TYR* 1.3 83.8 - - - +
137A ASN* 1.3 70.2 + - - +
138A HIS 3.9 0.2 - - - -
139A GLN* 5.1 4.0 + - - +
156A ALA* 3.6 13.2 + - - +
157A VAL* 3.9 22.0 - - + +
160A ALA* 3.8 23.9 - - + +
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Residues in contact with ASN 137 (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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98A CYS* 3.6 30.7 - - - +
102A THR* 4.7 2.5 - - - +
115A LYS* 5.0 0.7 + - - -
132A HIS 3.2 18.6 + - - -
133A LEU* 3.1 7.8 + - - +
136A ARG* 1.3 88.8 + - - +
138A HIS* 1.3 88.3 + - + +
139A GLN* 3.7 2.6 + - - -
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Residues in contact with HIS 138 (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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102A THR* 2.7 41.5 + - + -
105A ILE* 3.7 20.9 - - + +
106A ASP* 4.9 3.1 - - - -
115A LYS* 3.1 29.4 + - - +
120A ILE* 6.2 0.2 - - + -
133A LEU* 3.1 29.3 + - + +
134A ALA* 3.1 10.5 + - - +
137A ASN* 1.3 102.7 + - + +
139A GLN* 1.3 61.3 + - - +
140A ASP* 3.0 18.9 + - - +
141A VAL* 3.3 34.8 + - + +
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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