Contacts of the helix formed by residues 103 - 118 (chain A) in PDB entry 5J3V
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 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLU* 2.8 39.5 + - - -
65A ARG* 6.2 0.4 - - - -
101A ASP* 3.0 7.7 + - - +
102A SER* 1.3 80.5 + - - +
104A PRO* 1.3 66.1 - - - +
105A LEU* 3.5 8.1 + - - +
106A ILE* 3.2 20.2 + - - +
107A ARG* 2.9 27.9 + - - +
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Residues in contact with PRO 104 (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 SER 3.3 7.1 - - - +
103A SER* 1.3 86.2 - - - +
105A LEU* 1.3 57.6 + - - +
107A ARG* 3.8 27.7 - - - +
108A ALA* 3.1 29.5 + - - +
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Residues in contact with LEU 105 (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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62A GLU* 4.0 32.3 - - + +
63A PRO* 4.1 9.9 - - + -
66A SER* 3.9 28.9 - - - +
103A SER* 3.1 9.2 + - - +
104A PRO* 1.3 79.4 - - - +
106A ILE* 1.3 57.2 + - + +
108A ALA* 3.7 4.1 + - + +
109A THR* 2.6 33.5 + - - +
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Residues in contact with ILE 106 (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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54A LEU* 3.9 18.4 - - + +
55A THR* 5.9 0.2 - - - -
62A GLU* 3.8 32.1 - - + +
65A ARG* 3.8 44.9 - - + +
66A SER* 4.1 6.7 - - - +
98A ASN* 5.9 2.5 - - + +
101A ASP* 3.7 22.2 - - - +
103A SER* 3.2 21.0 + - - +
105A LEU* 1.3 75.9 - - + +
107A ARG* 1.3 59.9 + - - +
109A THR* 3.1 5.6 + - - -
110A VAL* 2.9 35.6 + - + +
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Residues in contact with ARG 107 (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 ASN 5.0 0.2 - - - -
99A ILE* 5.4 0.7 - - - -
100A GLY* 3.8 19.3 - - - +
101A ASP* 3.1 34.7 + - - +
102A SER 3.6 10.3 + - - -
103A SER 2.9 13.1 + - - +
104A PRO* 3.8 26.5 - - - +
106A ILE* 1.3 77.5 - - - +
108A ALA* 1.3 58.2 + - - +
110A VAL* 3.3 6.8 + - - +
111A GLY* 2.8 26.3 + - - -
142A TYR* 5.6 0.6 - - - -
143A ASN* 3.0 43.6 + - - +
146A GLU* 3.5 29.0 + - - -
147A GLY* 4.6 12.1 - - - -
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Residues in contact with ALA 108 (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 PRO 3.1 16.5 + - - +
105A LEU* 4.1 5.6 - - + +
107A ARG* 1.3 79.5 - - - +
109A THR* 1.3 58.2 + - - +
111A GLY* 4.0 2.2 - - - +
112A ILE* 3.1 28.8 + - - +
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Residues in contact with THR 109 (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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54A LEU* 3.9 14.4 - - + -
66A SER* 2.9 40.7 + - - +
69A GLY* 3.9 22.2 - - - -
70A LEU* 4.0 11.5 - - + +
105A LEU* 2.6 21.4 + - - +
106A ILE 3.1 9.8 + - - -
108A ALA* 1.3 76.9 - - - +
110A VAL* 1.3 63.8 + - - +
112A ILE* 3.2 20.6 - - - +
113A LEU* 3.4 11.1 + - - +
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Residues in contact with VAL 110 (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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54A LEU* 4.0 19.3 - - + -
55A THR* 4.7 4.0 - - + -
95A CYS* 3.2 38.8 - - + +
98A ASN* 4.0 30.7 - - + +
99A ILE* 4.5 3.8 - - + +
106A ILE* 2.9 27.5 + - + +
107A ARG 3.6 5.4 - - - +
109A THR* 1.3 77.2 - - - +
111A GLY* 1.3 63.4 + - - +
113A LEU* 3.1 20.1 + - - +
114A ILE* 3.3 17.6 + - + +
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Residues in contact with GLY 111 (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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99A ILE* 6.3 0.2 - - - -
107A ARG 2.8 16.9 + - - -
108A ALA* 4.0 2.5 - - - -
109A THR 3.4 0.2 - - - -
110A VAL* 1.3 79.4 - - - +
112A ILE* 1.3 58.5 + - - +
114A ILE* 3.4 10.9 + - - +
115A THR* 3.2 30.2 + - - +
147A GLY* 5.3 5.6 - - - -
151A ALA* 4.7 7.0 - - - +
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Residues in contact with ILE 112 (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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70A LEU* 4.1 12.1 - - + -
73A LYS* 3.6 34.5 - - + -
108A ALA 3.1 15.9 + - - +
109A THR* 3.2 21.3 - - - +
111A GLY* 1.3 73.5 - - - +
113A LEU* 1.3 61.3 + - + +
115A THR* 3.1 15.7 + - - +
116A THR* 2.5 33.6 + - - +
154A LYS* 5.8 4.3 - - - +
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Residues in contact with LEU 113 (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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51A ILE* 4.2 0.4 - - + -
54A LEU* 3.6 30.1 - - + -
69A GLY 3.4 22.0 - - - +
72A LEU* 3.9 25.8 - - + +
73A LYS* 3.7 27.1 - - + +
76A VAL* 5.1 5.4 - - + -
91A ILE* 4.8 0.4 - - + -
95A CYS* 3.8 22.0 - - - -
109A THR 3.5 10.8 - - - +
110A VAL* 3.1 9.3 + - - +
112A ILE* 1.3 80.8 - - + +
114A ILE* 1.3 59.7 + - - +
116A THR* 3.7 2.3 - - - -
117A ILE* 2.9 43.1 + - + +
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Residues in contact with ILE 114 (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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95A CYS* 3.6 23.8 - - + +
96A LEU* 4.1 4.9 - - + -
99A ILE* 3.6 37.7 - - + -
110A VAL* 3.3 17.2 + - + +
111A GLY* 3.7 11.0 - - - +
113A LEU* 1.3 76.0 - - - +
115A THR* 1.3 58.2 + - + +
117A ILE* 4.8 0.9 - - - -
118A ALA* 3.1 28.4 + - - +
126A TRP* 3.9 16.4 - - + -
129A LEU* 3.8 29.4 - - + -
133A LEU* 4.8 8.5 - - + -
147A GLY 6.0 0.4 - - - +
151A ALA* 4.9 10.1 - - + -
155A ILE* 5.3 2.2 - - + -
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Residues in contact with THR 115 (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 GLY 3.2 15.3 + - - +
112A ILE* 3.1 23.7 + - - +
114A ILE* 1.3 76.5 - - - +
116A THR* 1.3 57.6 + - - +
118A ALA* 4.1 4.0 - - - +
119A SER* 3.1 25.3 + - - -
150A GLY 4.8 0.7 - - - +
151A ALA* 3.7 27.8 - - + +
154A LYS* 3.6 42.6 + - + +
155A ILE* 4.9 6.4 - - + +
158A ASP* 4.0 5.4 - - - +
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Residues in contact with THR 116 (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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73A LYS* 3.7 22.2 - - + +
76A VAL* 4.1 16.3 - - + +
77A LYS* 3.6 33.4 - - + +
112A ILE* 2.5 27.1 + - - +
113A LEU* 3.7 4.3 - - - -
114A ILE 3.2 0.4 - - - -
115A THR* 1.3 76.8 + - - +
117A ILE* 1.3 64.7 + - - +
118A ALA 3.2 1.3 - - - -
119A SER* 3.0 12.7 + - - -
120A LYS* 3.1 19.3 + - + +
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Residues in contact with ILE 117 (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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76A VAL* 3.9 31.4 - - + -
80A PHE* 4.4 15.9 - - + -
88A THR* 5.1 2.2 - - + -
91A ILE* 3.8 32.5 - - + +
92A LYS* 3.8 36.3 - - + +
95A CYS* 5.3 1.6 - - - -
113A LEU* 2.9 27.0 + - + +
114A ILE* 5.2 0.2 - - - -
116A THR* 1.3 75.6 - - - +
118A ALA* 1.3 58.0 + - - +
121A GLY* 2.8 29.2 + - - +
122A GLU 4.8 0.3 - - - +
126A TRP* 3.9 17.0 - - + -
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Residues in contact with ALA 118 (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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114A ILE 3.1 20.6 + - - +
115A THR* 4.1 4.9 - - - +
117A ILE* 1.3 73.3 - - - +
119A SER* 1.3 58.2 + - - +
121A GLY 2.9 15.8 - - - +
122A GLU* 4.3 4.4 - - - -
123A LEU* 3.8 26.5 + - + +
126A TRP* 4.5 4.7 - - + -
129A LEU* 3.6 27.1 - - + -
155A ILE* 4.8 7.9 - - + -
159A SER* 4.7 6.6 + - - -
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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