Contacts of the helix formed by residues 124 - 144 (chain J) in PDB entry 5A31
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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125J GLN* 1.3 63.7 + - - +
126J SER* 3.4 3.7 - - - +
127J SER* 2.6 32.0 + - - +
128J ILE* 2.9 32.7 + - - +
16K GLN* 5.3 2.7 - - - -
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Residues in contact with GLN 125 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J SER* 1.3 78.5 - - - +
126J SER* 1.3 57.2 + - - +
128J ILE* 3.7 8.0 - - - +
129J LYS* 3.0 28.6 + - - +
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Residues in contact with SER 126 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J SER 3.4 1.9 - - - +
125J GLN* 1.3 74.9 - - - +
127J SER* 1.3 66.9 + - - +
129J LYS* 3.2 9.5 + - - +
130J SER* 3.1 23.1 + - - -
159J LEU* 4.9 13.2 - - - +
160J ASP* 6.1 0.4 - - - -
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Residues in contact with SER 127 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124J SER* 2.6 30.4 + - - +
126J SER* 1.3 78.5 - - - +
128J ILE* 1.3 56.4 + - - +
130J SER* 2.6 23.4 + - - -
131J SER* 2.9 15.2 + - - -
160J ASP* 4.3 13.9 - - - +
9K ARG* 4.9 11.7 - - - -
16K GLN* 3.3 35.5 + - - -
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Residues in contact with ILE 128 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J GLU* 5.1 10.8 - - + +
71J ALA* 4.7 29.2 - - + +
74J TYR* 5.3 11.8 - - + -
124J SER* 2.9 33.0 + - - +
125J GLN* 3.7 7.0 - - - +
127J SER* 1.3 80.9 + - - +
129J LYS* 1.3 62.4 + - - +
131J SER* 3.0 8.1 + - - +
132J ILE* 3.0 33.2 + - + +
16K GLN* 5.4 9.9 - - + +
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Residues in contact with LYS 129 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J GLU* 5.3 8.7 - - - +
125J GLN 3.0 14.3 + - - +
126J SER* 3.5 11.9 - - - +
128J ILE* 1.3 78.8 - - - +
130J SER* 1.3 52.4 + - - +
132J ILE* 3.1 14.3 - - + +
133J CYS* 2.7 33.7 - - - -
159J LEU* 3.9 24.5 - - + +
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Residues in contact with SER 130 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126J SER 3.1 8.0 + - - -
127J SER 2.6 16.1 + - - -
129J LYS* 1.3 73.8 - - - +
131J SER* 1.3 71.6 + - - +
133J CYS* 2.9 8.7 + - - +
134J LEU* 2.9 24.0 + - - -
156J ALA* 3.7 14.4 - - - +
159J LEU* 3.6 30.2 - - - +
160J ASP* 3.4 30.9 + - - +
163J CYS* 5.7 2.9 - - - +
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Residues in contact with SER 131 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J TYR* 4.2 14.1 + - - -
127J SER 2.9 15.5 + - - -
128J ILE* 3.0 17.5 + - - +
130J SER* 1.3 83.5 + - - +
132J ILE* 1.3 55.7 + - - +
134J LEU* 3.1 14.5 - - - +
135J LEU* 2.9 27.2 + - - +
160J ASP* 6.0 0.2 - - - -
163J CYS* 6.1 2.5 - - - -
16K GLN* 4.9 6.1 + - - +
18K GLN* 3.3 31.1 - - - +
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Residues in contact with ILE 132 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70J GLU* 4.5 20.9 - - + +
73J ARG* 4.2 23.6 - - - +
74J TYR* 3.9 43.5 - - + +
93J LEU* 3.6 27.3 - - + +
128J ILE* 3.0 18.6 + - + +
129J LYS* 3.1 27.6 - - + +
131J SER* 1.3 77.2 + - - +
133J CYS* 1.3 64.8 + - - +
135J LEU* 3.3 1.8 + - + +
136J ARG* 3.1 22.6 + - - +
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Residues in contact with CYS 133 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129J LYS* 2.7 34.3 - - - -
130J SER 2.9 8.5 + - - +
132J ILE* 1.3 75.5 - - - +
134J LEU* 1.3 67.1 + - - +
136J ARG* 3.2 21.6 + - - +
137J GLY 3.1 4.7 + - - -
152J SER* 2.8 29.0 + - - +
155J GLU* 4.8 7.6 - - + -
156J ALA* 4.2 18.8 - - + +
159J LEU* 4.0 18.2 - - - -
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Residues in contact with LEU 134 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130J SER 2.9 11.8 + - - +
131J SER* 3.1 12.6 - - - +
133J CYS* 1.3 77.0 - - - +
135J LEU* 1.3 61.7 + - - +
137J GLY* 3.0 4.3 + - - -
138J LYS* 2.9 40.6 + - - +
152J SER 4.9 0.2 - - - -
153J TYR* 3.6 27.0 - - + -
156J ALA* 3.6 13.6 - - + +
163J CYS* 4.5 10.1 - - - -
165J GLU* 3.8 16.2 - - + +
166J ALA* 4.2 19.3 - - + +
169J LEU* 5.4 0.7 - - + -
18K GLN* 3.1 33.7 - - - +
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Residues in contact with LEU 135 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J TYR* 3.6 27.6 - - + +
77J ALA* 3.7 16.2 - - + -
78J ARG* 3.6 33.4 - - + +
81J TYR* 3.9 31.6 - - + -
93J LEU* 4.9 3.8 - - + -
131J SER 2.9 13.2 + - - +
132J ILE 3.7 7.0 - - - +
133J CYS 3.2 0.4 - - - -
134J LEU* 1.3 74.6 - - + +
136J ARG* 1.3 67.5 + - - +
138J LYS* 3.0 17.1 + - + +
139J ILE* 3.0 36.1 + - + +
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Residues in contact with ARG 136 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90J LEU* 4.0 14.1 - - + +
93J LEU* 3.7 43.6 + - + +
94J ASP* 4.8 3.4 - - - +
132J ILE* 3.1 15.2 + - - +
133J CYS* 3.4 32.3 + - - +
134J LEU 3.2 0.2 - - - -
135J LEU* 1.3 75.9 - - - +
137J GLY* 1.3 64.1 + - - +
139J ILE* 3.1 12.1 + - - +
140J TYR* 2.9 55.8 + - + -
152J SER* 3.7 12.4 + - - -
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Residues in contact with GLY 137 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133J CYS 3.1 4.4 + - - -
134J LEU 3.0 8.2 + - - -
136J ARG* 1.3 79.0 - - - +
138J LYS* 1.3 62.7 + - - +
140J TYR 3.1 2.6 + - - -
141J ASP 3.0 17.7 + - - -
149J ALA* 3.5 19.2 - - - +
152J SER* 3.2 21.9 + - - -
153J TYR* 3.6 13.7 + - - -
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Residues in contact with LYS 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74J TYR* 5.8 1.4 + - - -
78J ARG* 5.5 7.7 - - - +
81J TYR* 3.9 38.3 + - + +
134J LEU* 2.9 34.7 + - + +
135J LEU* 3.0 19.5 + - + +
137J GLY* 1.3 74.3 - - - +
139J ILE* 1.3 62.0 + - - +
141J ASP* 3.2 13.2 + - - +
142J ALA* 3.3 12.0 + - - +
153J TYR* 3.3 16.9 + - + +
165J GLU* 3.8 30.6 + - - -
169J LEU* 5.0 12.1 - - + -
18K GLN* 5.1 1.0 - - - +
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Residues in contact with ILE 139 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81J TYR* 3.8 28.0 - - + -
86J HIS* 4.4 19.7 - - + +
87J GLN 4.6 2.5 - - - +
89J ALA* 3.7 25.8 - - + +
90J LEU* 4.2 34.1 - - + +
93J LEU* 4.7 4.3 - - + -
135J LEU* 3.0 37.3 + - + +
136J ARG* 3.1 11.0 + - - +
138J LYS* 1.3 73.4 - - - +
140J TYR* 1.3 62.6 + - - +
142J ALA* 2.9 5.9 + - - +
143J LEU* 2.8 27.8 + - + +
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Residues in contact with TYR 140 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90J LEU* 3.4 39.5 - - + +
94J ASP* 5.7 0.9 + - - -
136J ARG* 2.9 51.0 + - + -
137J GLY* 3.1 7.2 + - - +
139J ILE* 1.3 76.6 - - - +
141J ASP* 1.3 61.7 + - - +
143J LEU* 3.4 9.3 + - + -
144J ASP 3.0 2.9 + - - -
145J ASN* 2.8 49.3 + - + +
148J LEU* 3.7 43.8 - - + +
149J ALA* 3.6 18.8 - - + -
152J SER* 4.4 1.8 - - - -
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Residues in contact with ASP 141 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137J GLY 3.0 7.6 + - - +
138J LYS* 3.4 10.3 - - + +
139J ILE 3.1 0.4 - - - -
140J TYR* 1.3 76.5 - - - +
142J ALA* 1.3 57.5 + - - +
144J ASP* 3.0 21.3 + - - +
145J ASN 5.0 0.2 - - - +
146J ARG* 3.3 27.2 - - - +
149J ALA* 3.8 7.6 - - - +
153J TYR* 3.0 36.7 + - - +
169J LEU* 4.0 4.4 - - + +
173J HIS* 5.4 2.2 - - - -
175J MET* 3.3 19.0 - - - +
332J THR* 4.2 17.8 - - + +
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Residues in contact with ALA 142 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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735F LYS* 3.2 19.9 + - - -
81J TYR* 4.3 6.1 - - + +
84J LYS* 5.0 4.1 + - - +
86J HIS* 3.4 41.4 - - + +
138J LYS 3.3 8.3 + - - +
139J ILE 2.9 10.1 + - - +
141J ASP* 1.3 78.9 - - - +
143J LEU* 1.3 58.2 + - - +
144J ASP 3.2 0.2 - - - -
331J LYS* 5.9 0.9 + - - -
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Residues in contact with LEU 143 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734F PRO* 3.2 24.4 - - + +
735F LYS* 3.7 12.3 - - - +
86J HIS* 3.5 32.8 - - + -
87J GLN* 3.9 38.8 - - + +
90J LEU* 4.1 19.7 - - + -
139J ILE* 2.8 14.0 + - + +
140J TYR* 3.7 15.5 - - + +
142J ALA* 1.3 76.7 - - - +
144J ASP* 1.3 65.8 + - - +
145J ASN* 3.3 7.4 - - + +
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Residues in contact with ASP 144 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
734F PRO* 3.6 15.7 - - + +
735F LYS* 3.8 33.4 - - + +
740F TYR* 5.5 2.9 + - - -
766F LEU* 5.5 3.8 - - - +
140J TYR 3.0 3.2 + - - -
141J ASP* 3.0 15.6 + - - +
142J ALA 3.2 0.4 - - - -
143J LEU* 1.3 81.3 - - - +
145J ASN* 1.3 58.8 + - - +
146J ARG* 2.7 47.6 + - - +
332J THR* 5.3 3.1 - - - +
362J GLN* 5.6 2.6 - - - +
365J LYS* 5.6 0.5 + - - -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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