Contacts of the helix formed by residues 121 - 139 (chain A) in PDB entry 5A72
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 121 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A ASN* 3.2 15.8 + - + +
119A THR 3.8 0.4 - - - +
120A LYS* 1.3 77.6 - - - +
122A PRO* 1.3 66.7 - - - +
123A SER* 2.9 25.6 + - - -
124A VAL* 3.0 18.4 + - + +
125A LEU* 2.9 25.1 + - - +
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Residues in contact with PRO 122 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 4.0 14.1 - - + -
120A LYS 3.3 9.4 - - - +
121A ASP* 1.3 90.7 - - - +
123A SER* 1.3 56.7 + - - +
125A LEU* 3.8 3.1 - - + -
126A MET* 3.0 27.9 + - - +
155A LEU* 3.5 25.9 - - + +
160A HIS* 3.4 44.2 - - + +
161A VAL 5.3 4.3 - - - +
162A VAL* 4.9 2.4 - - + +
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Residues in contact with SER 123 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ASP* 2.9 12.8 + - - -
122A PRO* 1.3 80.1 - - - +
124A VAL* 1.3 63.2 + - - +
126A MET* 3.3 7.5 + - - +
127A GLU* 3.2 33.5 + - - +
161A VAL 4.8 10.5 + - - -
162A VAL* 4.6 12.3 - - - +
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Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 3.6 33.8 - - + +
118A ASN* 3.2 37.7 - - + +
119A THR* 4.2 2.7 - - + +
121A ASP* 3.0 18.5 + - + +
123A SER* 1.3 74.7 - - - +
125A LEU* 1.3 65.8 + - - +
126A MET 3.1 1.6 - - - -
127A GLU* 3.1 19.6 + - - +
128A ALA* 3.1 20.4 + - - +
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Residues in contact with LEU 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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30A ILE* 6.4 0.2 - - + -
38A LEU* 3.7 36.1 - - + +
40A TYR* 3.9 24.9 - - + +
41A GLN* 5.0 0.2 - - - -
42A VAL* 3.7 26.0 - - + +
119A THR* 3.9 28.8 - - + +
121A ASP 2.9 13.5 + - - +
122A PRO* 3.7 9.2 - - + +
123A SER 3.5 0.2 - - - -
124A VAL* 1.3 75.9 - - - +
126A MET* 1.3 57.4 + - - +
128A ALA* 3.4 1.7 + - - +
129A ALA* 2.9 26.0 + - + +
151A VAL* 4.2 22.7 - - + -
155A LEU* 4.5 4.5 - - + -
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Residues in contact with MET 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 PRO 3.0 18.2 + - - +
123A SER 3.4 6.7 - - - +
125A LEU* 1.3 76.4 - - - +
127A GLU* 1.3 65.5 + - + +
129A ALA* 3.3 4.2 + - + +
130A LEU* 3.0 41.9 + - + +
148A ALA* 3.4 29.4 - - + +
151A VAL* 4.3 9.9 - - + -
152A ARG* 3.6 59.0 - - + +
155A LEU* 4.3 6.5 - - + -
162A VAL* 3.4 27.1 - - + -
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Residues in contact with GLU 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115A LYS* 2.6 44.7 + - - +
123A SER* 3.2 25.0 + - - +
124A VAL* 3.1 18.8 + - - +
126A MET* 1.3 76.5 - - + +
128A ALA* 1.3 64.2 + - - +
130A LEU* 3.0 14.6 + - + +
131A LEU* 2.9 23.7 + - - +
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Residues in contact with ALA 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A VAL* 3.8 23.3 - - + +
112A ILE* 4.0 15.5 - - + +
115A LYS* 3.9 18.9 - - + +
116A LEU* 4.9 0.7 - - + -
119A THR* 4.7 7.2 - - + -
124A VAL 3.1 8.9 + - - +
125A LEU* 3.6 11.0 - - - +
127A GLU* 1.3 78.4 - - - +
129A ALA* 1.3 58.5 + - - +
131A LEU* 3.1 7.4 + - - +
132A ALA* 2.8 28.8 + - - +
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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
----------------------------------------------------------
30A ILE* 3.8 25.2 - - + +
42A VAL* 4.1 11.4 - - + -
125A LEU* 2.9 18.1 + - + +
126A MET* 3.7 5.8 - - + +
128A ALA* 1.3 72.1 - - - +
130A LEU* 1.3 66.1 + - - +
132A ALA* 3.4 3.7 + - - +
133A ASP* 3.2 17.0 + - - +
148A ALA* 3.7 16.0 - - + +
151A VAL* 4.1 20.6 - - + -
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Residues in contact with LEU 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 MET* 3.0 30.4 + - + +
127A GLU* 3.0 12.5 + - + +
129A ALA* 1.3 78.1 - - - +
131A LEU* 1.3 62.5 + - + +
133A ASP* 3.3 19.0 + - + +
134A LYS* 3.4 9.1 + - - +
148A ALA* 3.7 18.8 - - + -
152A ARG* 4.2 29.6 - - - +
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Residues in contact with LEU 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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108A LEU* 4.0 28.0 - - + +
111A GLN* 3.7 30.7 - - + -
112A ILE* 3.7 23.3 - - + +
115A LYS* 4.4 20.4 - - + -
127A GLU 2.9 12.0 + - - +
128A ALA* 3.5 7.9 - - - +
130A LEU* 1.3 74.6 - - + +
132A ALA* 1.3 58.7 + - - +
134A LYS* 2.7 37.3 + - + +
135A VAL* 3.1 12.6 + - + +
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Residues in contact with ALA 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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28A ALA* 3.7 32.9 - - + +
29A GLN 4.7 0.2 - - - -
30A ILE* 4.2 16.2 - - + -
42A VAL* 4.1 13.5 - - + -
112A ILE* 3.6 8.4 - - - +
128A ALA 2.8 19.1 + - - +
129A ALA 3.6 7.2 - - - +
130A LEU 3.4 0.2 - - - -
131A LEU* 1.3 73.0 - - - +
133A ASP* 1.3 62.3 + - - +
135A VAL* 3.4 4.9 + - - +
136A GLY 3.3 15.6 + - - -
144A ARG* 4.0 5.2 + - - +
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30A ILE* 4.6 2.4 - - - +
129A ALA 3.2 9.7 + - - +
130A LEU* 3.4 14.1 - - + +
131A LEU 3.0 0.6 - - - -
132A ALA* 1.3 77.5 - - - +
134A LYS* 1.3 64.0 + - + +
136A GLY* 3.1 11.8 + - - +
137A LEU* 3.2 19.0 + - + +
144A ARG* 4.9 5.1 + - - +
146A ILE 4.5 1.4 - - - +
147A LEU* 3.3 32.6 - - - +
148A ALA* 3.2 32.4 + - - +
149A GLU* 4.8 3.1 + - - +
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Residues in contact with LYS 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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108A LEU* 3.9 20.2 - - + +
130A LEU 3.4 7.3 + - - +
131A LEU* 2.7 28.4 + - + +
133A ASP* 1.3 77.0 - - + +
135A VAL* 1.3 60.2 + - - +
137A LEU* 3.5 25.0 + - + +
138A LEU* 3.6 15.8 + - - +
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Residues in contact with VAL 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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26A ILE 4.1 6.5 - - - +
27A ASN* 3.8 20.0 - - - +
28A ALA* 4.0 23.1 - - + +
105A GLN* 3.8 21.8 - - + -
108A LEU* 3.8 31.2 - - + -
109A VAL* 4.3 9.6 - - + +
112A ILE* 4.6 1.8 - - + -
131A LEU 3.1 12.9 + - - +
132A ALA* 3.6 7.4 - - - +
133A ASP 3.2 0.2 - - - -
134A LYS* 1.3 75.5 - - - +
136A GLY* 1.3 58.8 + - - +
138A LEU* 2.9 25.9 + - - +
139A THR* 3.3 8.4 - - + +
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Residues in contact with GLY 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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132A ALA 3.3 4.8 + - - -
133A ASP 3.1 8.9 + - - -
135A VAL* 1.3 79.3 - - - +
137A LEU* 1.3 60.6 + - - +
138A LEU 3.2 0.2 - - - -
139A THR* 3.4 23.4 + - - +
141A GLY* 5.0 3.3 + - - +
144A ARG* 3.0 31.8 + - - +
517C C 4.2 1.5 + - - -
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Residues in contact with LEU 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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133A ASP* 3.2 14.9 + - + +
134A LYS* 3.8 22.4 - - + +
135A VAL 3.2 1.2 - - - -
136A GLY* 1.3 77.4 - - - +
138A LEU* 1.3 64.0 + - + +
139A THR 3.4 5.0 + - - +
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Residues in contact with LEU 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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104A ALA* 3.6 32.1 - - + -
105A GLN* 3.9 30.6 + - + +
108A LEU* 4.0 22.7 - - + -
134A LYS 3.6 8.1 - - - +
135A VAL 2.9 9.2 + - - +
137A LEU* 1.3 81.6 - - + +
139A THR* 1.3 61.2 + - - +
140A ASP* 5.2 1.7 - - - +
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Residues in contact with THR 139 (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 CYS* 5.7 0.2 - - - -
26A ILE 4.6 4.5 - - - +
27A ASN* 4.2 12.3 - - + +
105A GLN* 4.4 13.9 - - - +
135A VAL* 3.3 21.7 + - + +
136A GLY 3.4 12.2 + - - +
137A LEU 3.4 5.6 - - - +
138A LEU* 1.3 82.7 - - - +
140A ASP* 1.3 62.2 + - - +
141A GLY 3.1 13.4 + - - +
516C A 3.6 22.8 - - - +
517C C 2.6 29.3 + - - +
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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
------------------------------------------------------------
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