Contacts of the helix formed by residues 109 - 129 (chain B) in PDB entry 1J38
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 PRO 109 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B LYS* 4.3 3.1 - - - +
107B ALA 3.7 1.3 - - - +
108B LEU* 1.3 83.7 - - + +
110B GLU* 1.3 66.8 + - - +
111B ASP* 3.2 11.4 - - - +
112B ASP* 2.7 47.4 + - - +
113B TYR 3.1 9.5 + - - -
190B LYS* 4.3 9.2 - - - +
194B LEU* 4.1 13.7 - - + -
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Residues in contact with GLU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B LYS* 4.1 29.4 + - + +
74B LYS* 3.4 20.8 - - - +
108B LEU 4.4 0.2 - - - -
109B PRO* 1.3 70.4 - - - +
111B ASP* 1.3 68.5 + - - +
113B TYR* 3.6 6.4 + - - +
114B ALA* 3.3 22.4 + - + +
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Residues in contact with ASP 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 3.6 19.9 - - - +
110B GLU* 1.3 82.1 + - - +
112B ASP* 1.3 91.6 + - - +
114B ALA* 3.5 4.4 + - - +
115B GLU* 3.2 20.9 + - - +
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Residues in contact with ASP 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B LEU* 3.7 18.8 - - + -
109B PRO* 2.7 31.0 + - - +
111B ASP* 1.3 106.4 - - - +
113B TYR* 1.3 52.1 + - - +
115B GLU* 2.6 16.1 + - - +
116B LEU* 2.6 34.1 + - - +
183B ARG* 4.5 10.6 + - - -
187B LEU* 4.0 15.6 - - + +
190B LYS* 2.8 26.3 + - - +
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Residues in contact with TYR 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B GLU* 5.0 1.6 + - - -
66B SER* 3.4 34.4 + - - -
67B ALA* 4.0 6.1 - - + -
70B ALA* 3.6 22.7 - - + +
74B LYS* 5.6 0.9 - - - +
105B TYR* 3.0 49.6 - + + +
106B ALA* 4.1 5.8 - - + +
108B LEU* 4.2 9.5 - - + +
109B PRO 3.1 9.3 + - - +
110B GLU* 3.8 11.2 - - - +
112B ASP* 1.3 78.1 - - - +
114B ALA* 1.3 58.0 + - + +
116B LEU* 3.1 8.5 + - + +
117B LEU* 2.8 67.4 + - + +
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Residues in contact with ALA 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67B ALA* 6.0 4.0 - - + -
110B GLU* 3.3 14.8 + - + +
111B ASP* 3.9 4.5 - - - +
112B ASP 3.2 0.8 - - - -
113B TYR* 1.3 80.4 - - + +
115B GLU* 1.3 58.5 + - - +
117B LEU* 3.5 15.8 + - + +
118B ASP* 3.0 30.7 + - - +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ASP* 3.2 13.2 + - - +
112B ASP* 2.6 21.3 + - - +
114B ALA* 1.3 71.5 - - - +
116B LEU* 1.3 52.6 + - - -
118B ASP* 3.4 6.2 - - + +
119B THR* 2.7 50.1 + - + +
183B ARG* 2.6 50.1 + - - +
187B LEU* 4.3 4.4 - - + +
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Residues in contact with LEU 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 3.4 52.9 - - + -
108B LEU* 3.9 11.9 - - + -
112B ASP 2.6 14.3 + - - +
113B TYR* 3.1 13.2 + - + +
115B GLU* 1.3 69.4 - - - +
117B LEU* 1.3 68.1 + - + +
118B ASP 2.9 1.3 - - - -
119B THR* 3.3 3.5 + - - +
120B LEU* 2.8 39.6 + - + +
184B TYR* 4.1 29.4 - - + +
187B LEU* 3.9 28.9 - - + +
188B ASN 5.0 1.1 - - - +
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Residues in contact with LEU 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ASN* 3.4 48.6 - - + +
66B SER* 3.9 13.7 - - - +
67B ALA* 4.3 5.8 - - + +
113B TYR* 2.8 65.9 + - + +
114B ALA* 3.6 13.7 - - + +
116B LEU* 1.3 77.2 - - + +
118B ASP* 1.3 57.0 + - - +
120B LEU* 3.6 12.5 - - + +
121B SER* 2.8 32.3 + - - -
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Residues in contact with ASP 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B GLU* 5.2 5.5 - - - +
63B ASN* 5.2 5.4 + - - +
114B ALA 3.0 18.2 + - - +
115B GLU* 3.4 9.4 - - + +
116B LEU 2.8 1.2 + - - -
117B LEU* 1.3 74.8 - - - +
119B THR* 1.3 68.4 + - + +
120B LEU 2.9 0.9 - - - -
121B SER* 2.6 20.0 + - - -
122B ALA* 2.7 14.4 + - - +
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Residues in contact with THR 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 2.7 42.5 + - + +
116B LEU* 3.9 7.4 + - - +
118B ASP* 1.3 73.7 - - + +
120B LEU* 1.3 63.2 + - - +
122B ALA* 3.3 5.3 + - - +
123B MET* 3.2 27.5 + - - +
180B GLN* 3.6 36.2 + - - +
183B ARG* 4.1 17.9 - - + -
184B TYR* 4.0 14.4 + - - +
187B LEU* 5.0 0.7 - - + -
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Residues in contact with LEU 120 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B TYR* 4.8 7.0 - - + -
116B LEU* 2.8 35.6 + - + +
117B LEU* 3.6 12.1 - - + +
119B THR* 1.3 76.7 + - - +
121B SER* 1.3 65.7 + - - +
123B MET* 3.0 28.4 + - + +
124B GLU* 3.1 15.3 + - - +
184B TYR* 3.7 30.3 - - + -
499B SER 4.5 2.6 - - - +
500B ALA 5.6 1.8 - - - +
501B ASP* 4.0 31.4 - - + +
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Residues in contact with SER 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50B TYR* 5.0 1.6 + - - -
59B GLU* 3.7 29.4 - - - +
62B LYS* 4.7 8.9 + - - +
63B ASN* 3.0 28.0 + - - -
117B LEU 2.8 17.1 + - - -
118B ASP* 2.6 13.1 + - - -
120B LEU* 1.3 72.5 - - - +
122B ALA* 1.3 52.7 + - - -
124B GLU* 3.9 9.0 - - - +
125B SER* 2.7 36.3 + - - -
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Residues in contact with ALA 122 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASP* 2.7 16.4 + - - +
119B THR* 3.4 11.2 - - - +
121B SER* 1.3 74.7 - - - +
123B MET* 1.3 56.8 + - - +
125B SER* 3.3 5.5 + - - -
126B ASN* 3.0 29.6 + - - +
177B VAL* 4.6 2.1 - - - +
180B GLN* 3.4 26.0 - - + +
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Residues in contact with MET 123 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B THR 3.2 14.4 - - - +
120B LEU* 3.0 27.3 + - + +
122B ALA* 1.3 73.2 - - - +
124B GLU* 1.3 60.3 + - - +
126B ASN* 3.2 2.7 + - - +
127B PHE* 2.9 30.5 + - - +
177B VAL* 3.7 19.9 - - + +
180B GLN* 3.5 13.5 - - + -
181B PHE* 3.6 38.6 - - + -
184B TYR* 4.1 19.3 - - + -
493B PRO* 5.8 0.2 - - - -
498B ILE 4.0 11.9 - - - +
499B SER* 3.2 46.3 + - - +
501B ASP 5.0 1.3 - - - +
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Residues in contact with GLU 124 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 3.2 14.8 - - + -
51B ARG* 4.5 15.8 + - - -
62B LYS* 2.6 33.5 + - - -
120B LEU 3.1 12.4 + - - +
121B SER* 3.9 5.9 - - - +
123B MET* 1.3 80.3 - - - +
125B SER* 1.3 62.9 + - - +
127B PHE* 3.4 5.8 + - - +
128B ALA* 3.2 22.3 + - - +
335B VAL* 4.7 16.5 - - + +
496B TYR* 5.3 7.5 + - + +
499B SER* 4.0 9.8 + - - +
500B ALA* 4.5 23.1 - - + +
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Residues in contact with SER 125 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B TYR* 3.4 24.0 + - - -
54B ILE* 4.6 2.5 - - - -
59B GLU* 4.3 8.6 + - - -
121B SER 2.7 21.7 + - - -
122B ALA* 3.3 6.4 + - - -
124B GLU* 1.3 76.3 - - - +
126B ASN* 1.3 70.0 + - - +
128B ALA* 3.3 4.6 + - - -
129B LYS* 2.9 45.7 + - - +
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Residues in contact with ASN 126 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122B ALA 3.0 22.6 + - - +
123B MET* 3.2 7.4 + - - +
125B SER* 1.3 79.3 + - - +
127B PHE* 1.3 65.5 + - - +
129B LYS* 3.3 10.1 + - - +
130B VAL* 3.4 12.4 + - - +
172B LYS 2.9 22.2 + - - +
173B ALA* 3.9 11.1 - - - +
176B ALA* 4.0 21.8 + - - +
177B VAL* 4.7 11.0 - - + +
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Residues in contact with PHE 127 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B MET 2.9 16.3 + - - +
124B GLU* 3.6 5.8 - - - +
126B ASN* 1.3 82.3 + - - +
128B ALA* 1.3 68.2 + - + +
129B LYS 3.2 0.3 + - - -
130B VAL* 3.3 21.7 + - - +
145B LEU* 3.7 33.4 - - + +
169B PHE* 3.9 7.8 - + - -
173B ALA* 4.3 10.5 - - + +
263B TRP* 4.7 2.0 - + - -
337B HIS* 5.5 4.5 - - + -
493B PRO 3.7 4.5 - - - -
494B ALA 3.0 25.4 - - - -
496B TYR* 3.2 50.9 - + + -
499B SER* 3.7 25.4 - - - +
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Residues in contact with ALA 128 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 3.7 17.7 - - + +
124B GLU 3.2 14.0 + - - +
125B SER 3.3 2.4 + - - +
127B PHE* 1.3 85.8 - - + +
129B LYS* 1.3 60.4 + - - +
130B VAL 3.4 2.8 + - - +
131B LYS* 4.9 5.2 + - - -
144B ALA* 5.8 2.1 - - - +
333B ASP* 5.2 3.3 - - - +
334B LEU 3.6 25.7 + - - +
335B VAL* 4.0 13.2 - - + -
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Residues in contact with LYS 129 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54B ILE* 4.0 28.9 + - + +
56B ASP* 5.1 8.9 + - - -
125B SER* 2.9 28.3 + - - +
126B ASN* 3.3 5.1 + - - +
127B PHE 3.2 0.2 - - - -
128B ALA* 1.3 78.4 - - + +
130B VAL* 1.3 67.1 + - - +
131B LYS* 3.4 14.9 + - - +
333B ASP* 3.2 30.2 - - + +
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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