Contacts of the helix formed by residues 118 - 131 (chain A) in PDB entry 1JSA
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 LYS 118 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A SER* 1.3 86.1 + - - +
119A ASN* 1.3 65.9 + - - +
121A VAL* 3.3 8.5 + - - +
122A LEU* 2.9 25.9 + - + +
151A ALA* 6.0 3.2 - - + +
155A TRP* 4.4 34.9 - - + +
164A ASP* 5.8 7.0 - - + +
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Residues in contact with ASN 119 (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 ASP* 4.9 2.2 + - - -
117A SER* 3.2 8.1 + - - +
118A LYS* 1.3 77.0 - - - +
120A GLU* 1.3 63.8 + - + +
122A LEU* 2.6 32.2 + - - +
123A GLU* 2.6 37.9 + - - +
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Residues in contact with GLU 120 (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 TYR 3.7 14.5 - - - +
109A ASP* 2.7 15.8 - - - +
110A VAL* 4.6 7.4 - - + +
111A ASP* 2.4 47.8 - - - +
113A ASN* 3.9 1.2 - - - +
115A THR 4.0 0.3 - - - +
116A ILE* 4.0 7.0 - - + -
117A SER* 3.7 25.1 + - - +
119A ASN* 1.3 85.3 - - + +
121A VAL* 1.3 65.1 + - - +
122A LEU 3.0 0.9 + - - -
123A GLU* 3.0 19.1 + - - +
124A ILE* 3.2 16.6 + - - +
501A CA 2.5 20.9 - - - -
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Residues in contact with VAL 121 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108A TYR* 4.8 17.5 - - + -
116A ILE* 3.2 22.7 - - + -
117A SER 2.8 24.9 + - - +
118A LYS* 3.5 7.6 - - - +
119A ASN 3.1 0.4 - - - -
120A GLU* 1.3 77.2 - - - +
122A LEU* 1.3 55.3 + - - +
124A ILE* 4.1 0.7 - - - +
125A VAL* 2.6 52.2 + - + +
151A ALA* 5.4 9.4 - - + +
154A ILE* 4.5 19.3 - - + -
155A TRP* 4.1 19.1 - - + +
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Residues in contact with LEU 122 (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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118A LYS* 2.9 16.0 + - + +
119A ASN* 2.6 24.3 + - - +
121A VAL* 1.3 70.9 - - - +
123A GLU* 1.3 75.0 + - - +
125A VAL* 3.1 4.3 + - + +
126A THR* 2.8 40.9 + - - +
147A PRO* 4.1 24.7 - - + +
148A GLU* 4.4 23.6 - - + +
151A ALA* 4.9 12.1 - - + -
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Residues in contact with GLU 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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67A HIS* 4.2 16.3 + - + +
110A VAL* 5.0 3.1 - - + -
119A ASN* 2.6 45.0 + - - +
120A GLU* 3.0 8.6 + - - +
122A LEU* 1.3 88.3 - - - +
124A ILE* 1.3 74.9 + - + +
125A VAL 2.9 0.7 + - - -
126A THR* 3.0 5.0 + - - -
127A ALA* 2.9 22.9 + - - +
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Residues in contact with ILE 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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64A TYR* 5.3 4.5 - - + -
67A HIS* 3.6 23.3 - - + +
107A LEU* 3.8 29.6 - - + +
108A TYR* 3.1 48.5 - - + +
110A VAL* 3.0 36.3 - - + -
120A GLU 3.2 9.9 + - - +
121A VAL 4.4 0.2 - - - +
123A GLU* 1.3 81.2 - - + +
125A VAL* 1.3 56.9 + - - +
127A ALA* 3.8 6.9 - - - +
128A ILE* 3.0 35.6 + - + +
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Residues in contact with VAL 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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108A TYR* 5.1 7.9 - - + +
121A VAL* 2.6 35.5 + - + +
122A LEU* 3.3 6.7 - - - +
123A GLU 2.9 1.0 + - - -
124A ILE* 1.3 76.2 - - - +
126A THR* 1.3 67.7 + - - +
128A ILE* 3.3 9.7 + - + +
129A PHE* 3.1 23.1 + - + +
147A PRO* 3.8 33.7 - - + +
150A ARG* 4.7 15.5 - - + +
151A ALA* 5.2 3.4 - - - +
154A ILE* 3.4 31.0 - - + -
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Residues in contact with THR 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 LEU* 2.8 23.6 + - - +
123A GLU* 3.7 4.7 - - - -
125A VAL* 1.3 74.5 - - - +
127A ALA* 1.3 65.8 + - - +
129A PHE* 2.9 22.4 + - + +
130A LYS* 3.2 17.2 + - - +
147A PRO* 2.9 37.1 - - + +
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Residues in contact with ALA 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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61A PRO* 5.8 0.3 - - - +
63A ALA* 3.7 29.8 - - + +
64A TYR* 3.9 10.2 - - + +
67A HIS* 3.7 26.5 - - + +
123A GLU 2.9 16.3 + - - +
124A ILE* 3.8 4.0 - - - +
126A THR* 1.3 78.3 - - - +
128A ILE* 1.3 65.5 + - - +
130A LYS* 2.8 21.5 + - - +
131A MET* 3.4 4.9 + - - +
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Residues in contact with ILE 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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64A TYR* 4.6 19.3 - - + -
108A TYR* 3.4 26.9 - - + +
124A ILE* 3.0 34.5 + - + +
125A VAL* 3.5 8.7 - - + +
126A THR 3.2 0.2 - - - -
127A ALA* 1.3 77.6 - - - +
129A PHE* 1.3 65.6 + - + +
131A MET* 3.1 19.4 + - + +
132A ILE* 3.2 21.6 + - + +
150A ARG* 5.0 11.0 - - - +
184A LEU 5.3 1.6 - - - +
185A ILE* 4.2 3.6 - - - +
186A GLN* 3.9 33.9 - - + +
187A PHE* 5.5 3.4 - - + -
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Residues in contact with PHE 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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125A VAL* 3.1 14.6 + - + +
126A THR* 2.9 19.2 + - + +
128A ILE* 1.3 80.4 - - + +
130A LYS* 1.3 61.4 + - + +
132A ILE* 2.9 40.0 + - + +
137A THR* 3.9 25.3 + - + -
140A LEU* 4.5 7.0 - - + -
144A GLU 3.8 11.4 - - - -
145A ASN* 3.2 37.2 - - - -
146A THR* 4.0 8.7 - - - -
147A PRO* 4.5 15.3 - - + -
150A ARG* 4.3 22.0 - - - -
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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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59A ALA* 3.8 7.1 - - - +
60A ASP* 3.8 30.4 + - + +
63A ALA* 4.1 17.0 - - + -
126A THR* 3.8 17.9 - - + +
127A ALA* 2.8 13.1 + - - +
129A PHE* 1.3 78.6 - - + +
131A MET* 1.3 63.6 + - - +
132A ILE 3.0 10.1 - - - +
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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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52A TYR* 4.8 4.5 - - + -
56A PHE* 3.9 30.7 - - + -
59A ALA* 2.6 31.0 - - - +
60A ASP 4.4 3.7 + - - +
61A PRO* 3.4 48.9 - - + -
64A TYR* 5.2 10.1 - - + -
127A ALA 3.4 4.2 + - - +
128A ILE* 3.1 17.8 + - + +
130A LYS* 1.3 78.9 - - - +
132A ILE* 1.3 60.9 + - + +
133A SER* 3.6 1.0 + - - -
186A GLN* 5.8 5.6 - - - +
188A GLU* 4.4 20.6 - - + +
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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