Contacts of the helix formed by residues 108 - 123 (chain A) in PDB entry 3SDI
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 108 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ILE* 4.5 0.2 - - - -
100A TYR* 3.5 24.2 - - + +
106A TYR 3.7 2.2 - - - +
107A PRO* 1.3 88.8 - - + +
109A THR* 1.3 66.2 + - - +
110A LYS* 3.4 7.2 - - + -
111A LEU* 3.1 29.8 + - + +
112A LEU* 3.1 9.9 + - - +
142A ASP* 3.3 30.5 - - + +
145A ASN* 3.8 12.3 - - - +
70I GLU* 3.6 17.9 - - - +
72I ARG* 6.1 1.3 - - - +
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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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74A ILE* 3.9 15.0 - - + +
107A PRO 3.7 1.4 + - - -
108A PRO* 1.3 69.2 - - - +
110A LYS* 1.3 64.3 + - - +
112A LEU* 3.1 3.6 + - - +
113A VAL* 2.9 22.9 + - - +
138A ILE* 4.3 19.5 - - + +
140A GLY* 3.3 41.0 - - - +
141A HIS 3.7 3.0 + - - -
142A ASP* 3.2 12.4 + - - +
147A SER* 3.7 16.3 - - + +
149A TYR* 3.9 21.8 - - + -
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Residues in contact with LYS 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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108A PRO* 4.5 11.2 - - + -
109A THR* 1.3 74.5 - - - +
111A LEU* 1.3 67.6 + - + +
113A VAL* 3.4 4.8 + - - +
114A SER* 2.9 28.6 + - - -
142A ASP* 4.9 0.4 + - - -
145A ASN* 3.5 35.9 + - - +
147A SER* 5.2 0.2 - - - +
149A TYR* 3.6 33.3 - - + +
157A TYR* 4.9 6.0 + - + -
63B THR* 6.0 5.5 - - + +
69I LYS 4.2 6.7 + - - +
70I GLU* 2.9 34.6 + - - +
71I GLU* 3.4 26.2 + - - +
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Residues in contact with LEU 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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100A TYR* 4.1 10.3 - - + -
107A PRO* 4.6 5.2 - - + -
108A PRO* 3.1 23.2 + - + +
110A LYS* 1.3 83.2 - - + +
112A LEU* 1.3 63.6 + - - +
114A SER* 3.2 13.6 - - - +
115A GLU* 3.1 29.4 + - + +
69I LYS* 3.6 42.8 - - + +
70I GLU* 3.3 41.7 - - + +
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Residues in contact with LEU 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* 4.2 20.9 - - + -
71A THR* 3.8 19.5 - - + -
74A ILE* 3.7 28.5 - - + -
92A SER 3.6 24.0 - - - +
95A VAL* 3.9 16.8 - - + -
96A ALA* 4.1 11.9 - - + -
107A PRO* 4.0 13.1 - - + +
108A PRO 3.1 11.1 + - - +
109A THR 3.8 5.4 - - - +
111A LEU* 1.3 74.0 - - - +
113A VAL* 1.3 66.3 + - + +
115A GLU* 3.0 7.4 + - + +
116A VAL* 3.0 33.9 + - + +
138A ILE* 5.8 1.8 - - + -
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Residues in contact with VAL 113 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A THR* 2.9 19.5 + - + +
110A LYS* 3.6 5.8 - - - +
112A LEU* 1.3 75.1 - - - +
114A SER* 1.3 56.2 + - - +
116A VAL* 3.1 9.9 + - - +
117A ALA* 2.8 32.7 + - - +
138A ILE* 3.8 31.4 - - + -
149A TYR* 3.7 30.7 - - + -
151A VAL* 3.8 10.8 - - + +
157A TYR* 3.6 39.7 - - + -
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Residues in contact with SER 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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110A LYS 2.9 15.5 + - - -
111A LEU* 3.2 23.7 - - - +
113A VAL* 1.3 78.1 - - - +
115A GLU* 1.3 58.4 + - - +
117A ALA* 3.6 2.9 - - - +
118A LYS* 3.2 25.1 + - - +
157A TYR* 3.8 19.5 + - - -
86B GLU* 3.8 16.8 + - - +
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Residues in contact with GLU 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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95A VAL* 3.8 39.5 - - + +
99A SER* 4.7 14.5 + - - -
111A LEU* 3.1 16.4 + - - +
112A LEU* 3.0 12.6 + - + +
114A SER* 1.3 76.1 - - - +
116A VAL* 1.3 64.0 + - - +
118A LYS* 3.2 21.3 + - - +
119A ILE* 3.1 26.4 + - - +
69I LYS* 4.9 10.9 + - - +
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Residues in contact with VAL 116 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A LEU* 5.3 0.9 - - + -
88A LEU* 4.2 15.9 - - + -
92A SER* 3.2 33.4 - - - +
95A VAL* 5.6 0.4 - - + -
112A LEU* 3.0 25.9 + - + +
113A VAL* 3.6 7.2 - - - +
115A GLU* 1.3 75.0 - - + +
117A ALA* 1.3 62.9 + - - +
119A ILE* 3.0 20.2 + - + +
120A MET* 3.0 18.1 + - - +
136A LEU* 3.8 26.9 - - + -
138A ILE* 4.3 13.0 - - + -
151A VAL* 5.3 2.0 - - + -
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Residues in contact with ALA 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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113A VAL 2.8 16.4 + - - +
114A SER 3.6 5.8 - - - +
116A VAL* 1.3 75.4 - - - +
118A LYS* 1.3 51.7 + - - +
120A MET* 3.2 3.6 + - - +
121A GLN* 2.7 36.6 + - - +
151A VAL* 4.0 15.1 - - + +
155A GLY* 3.1 27.7 - - - +
157A TYR* 3.4 22.0 - - + -
83B ALA* 5.9 0.2 - - - -
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Residues in contact with LYS 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 SER 3.2 11.2 + - - +
115A GLU* 3.2 24.7 + - - +
117A ALA* 1.3 78.6 - - - +
119A ILE* 1.3 57.6 + - + +
121A GLN* 3.4 7.3 + - - +
122A GLU* 3.0 60.8 + - - +
87B ILE* 4.3 20.4 - - + -
90B ASN* 5.8 4.2 - - - +
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Residues in contact with ILE 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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88A LEU* 3.6 24.5 - - + -
91A LYS* 4.2 47.6 - - + +
92A SER* 5.0 2.9 - - - +
95A VAL* 4.6 14.1 - - + -
115A GLU 3.1 18.9 + - - +
116A VAL* 3.0 14.1 + - - +
118A LYS* 1.3 77.4 - - + +
120A MET* 1.3 63.0 + - - +
122A GLU* 3.6 15.1 + - - +
123A ALA* 3.5 12.1 + - - +
132A PHE* 3.8 16.9 - - + -
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Residues in contact with MET 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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88A LEU* 4.0 16.4 - - + -
116A VAL* 3.0 18.2 + - - +
117A ALA 3.6 6.1 - - - +
119A ILE* 1.3 74.8 - - - +
121A GLN* 1.3 66.5 + - - +
123A ALA* 2.9 18.0 + - - +
124A THR* 3.5 8.8 + - - -
131A PRO* 5.5 0.2 - - - +
132A PHE* 3.9 27.9 + - + -
134A VAL* 3.5 39.9 - - + +
136A LEU* 4.5 4.3 - - + -
151A VAL* 3.8 27.6 - - - +
152A ASP 3.6 22.7 - - - +
153A PRO* 3.8 16.2 - - + +
155A GLY* 4.3 2.0 - - - -
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Residues in contact with GLN 121 (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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117A ALA 2.7 21.4 + - - +
118A LYS* 3.6 8.5 - - - +
120A MET* 1.3 72.0 - - - +
122A GLU* 1.3 67.4 + - - +
124A THR* 3.0 21.6 + - - -
125A GLN* 3.1 27.6 + - - +
154A SER 3.8 11.4 - - - +
155A GLY* 4.0 1.2 - - - -
83B ALA* 3.6 37.9 - - + +
84B ASP* 3.0 22.9 + - - +
87B ILE* 3.5 27.6 - - + +
130B ARG* 3.4 7.1 - - - +
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Residues in contact with GLU 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* 3.0 51.0 + - + +
119A ILE* 4.0 16.1 - - - +
120A MET 3.1 0.2 - - - -
121A GLN* 1.3 83.4 - - - +
123A ALA* 1.3 57.1 + - - +
124A THR 3.0 5.5 + - - -
125A GLN* 4.5 2.2 - - - +
126A SER* 2.9 44.1 + - - +
87B ILE* 4.9 4.8 - - + +
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Residues in contact with ALA 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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13A THR* 4.6 0.5 + - - -
119A ILE 3.5 2.6 + - - +
120A MET 2.9 11.6 + - - +
122A GLU* 1.3 77.1 - - - +
124A THR* 1.3 56.5 + - - +
125A GLN 3.6 0.2 - - - -
129A VAL* 3.6 24.6 - - + +
130A ARG 3.5 17.9 - - - +
131A PRO* 3.4 24.7 - - + +
132A PHE* 3.8 29.6 - - + -
125G GLN* 4.2 2.5 - - - +
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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
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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