Contacts of the helix formed by residues 102 - 123 (chain A) in PDB entry 4N41
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 ASP 102 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99A ASP* 2.6 25.4 + - + +
101A LYS* 1.3 72.6 - - - +
103A PRO* 1.3 65.5 - - - +
104A GLY* 3.9 6.6 + - - -
105A GLU* 3.2 36.2 + - - +
106A ARG* 2.8 34.0 + - - +
69B PRO* 4.8 13.2 - - - +
72B VAL* 5.4 0.9 - - - +
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Residues in contact with PRO 103 (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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101A LYS 3.2 10.9 - - - +
102A ASP* 1.3 91.9 - - - +
104A GLY* 1.3 57.2 + - - +
106A ARG* 3.8 24.7 + - - +
107A SER* 2.9 29.5 + - - -
69B PRO* 5.5 7.9 - - + -
71B GLU* 5.1 12.8 - - + -
72B VAL* 4.0 27.8 - - + -
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Residues in contact with GLY 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A ASP* 3.4 6.7 + - - -
103A PRO* 1.3 78.0 - - - +
105A GLU* 1.3 58.3 + - - +
107A SER* 3.1 10.2 + - - -
108A VAL* 3.0 31.2 + - - +
69B PRO* 5.6 3.2 - - - +
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Residues in contact with GLU 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96A ARG* 3.9 22.8 + - - +
97A PRO 4.0 6.8 - - - +
98A LEU* 3.2 34.3 - - + +
99A ASP* 2.5 42.6 + - - +
102A ASP* 3.2 28.0 + - - +
104A GLY* 1.3 72.7 - - - +
106A ARG* 1.3 60.7 + - - +
108A VAL* 3.0 13.2 + - + +
109A LEU* 2.9 24.1 + - - +
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Residues in contact with ARG 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP 4.2 1.0 + - - -
100A PRO* 2.7 31.1 + - + +
101A LYS 4.1 9.3 + - - -
102A ASP 2.8 19.4 + - - +
103A PRO* 3.8 27.5 + - - +
105A GLU* 1.3 72.9 - - - +
107A SER* 1.3 57.5 + - - +
109A LEU* 3.3 9.1 + - + +
110A SER* 2.9 33.7 + - - -
157A VAL* 3.2 28.9 - - + +
158A SER* 3.3 20.0 - - - +
159A ASP* 2.9 26.4 + - - +
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Residues in contact with SER 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103A PRO 2.9 15.2 + - - -
104A GLY* 3.2 15.5 - - - -
106A ARG* 1.3 76.0 - - - +
108A VAL* 1.3 57.2 + - - +
110A SER* 3.5 6.9 + - - -
111A ALA* 2.9 28.8 + - - +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A VAL* 4.0 10.0 - - + +
59A ARG 4.4 8.3 - - - +
60A MET* 4.1 23.6 - - + -
65A ALA* 4.0 25.8 - - + -
98A LEU* 3.7 17.3 - - + -
104A GLY 3.0 20.7 + - - +
105A GLU* 3.0 12.3 + - + +
107A SER* 1.3 73.5 - - - +
109A LEU* 1.3 66.8 + - - +
111A ALA* 3.1 8.1 + - - +
112A LEU* 3.0 25.5 + - + +
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Residues in contact with LEU 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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19A LEU* 3.9 8.5 - - + -
23A GLU 3.4 25.6 - - - +
24A LEU* 4.0 25.1 - - + -
26A PRO* 4.3 6.5 - - + -
67A TRP* 3.9 13.4 - - + -
98A LEU* 3.7 33.0 - - + -
100A PRO* 4.3 15.9 - - + -
105A GLU 2.9 9.7 + - - +
106A ARG* 3.3 12.3 + - - +
108A VAL* 1.3 75.3 - - - +
110A SER* 1.3 57.5 + - - +
112A LEU* 3.2 8.5 + - + +
113A ALA 2.9 22.7 + - - -
157A VAL* 3.7 24.3 - - + +
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Residues in contact with SER 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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106A ARG* 2.9 21.0 + - - +
107A SER* 3.7 8.0 - - - -
109A LEU* 1.3 73.6 - - - +
111A ALA* 1.3 59.8 + - - +
113A ALA* 3.1 4.1 + - - +
114A ARG* 2.9 35.9 + - - +
155A LEU 3.6 4.5 - - - +
156A TRP* 3.4 16.8 - - - +
157A VAL* 3.0 35.7 + - - +
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Residues in contact with ALA 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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58A VAL* 3.6 24.9 - - + +
59A ARG 5.8 0.2 - - - +
107A SER 2.9 18.2 + - - +
108A VAL* 3.5 6.1 - - - +
110A SER* 1.3 75.5 - - - +
112A LEU* 1.3 57.6 + - - +
114A ARG* 3.4 11.4 + - - +
115A ARG* 2.9 28.6 + - - +
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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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26A PRO* 4.0 19.7 - - + -
56A VAL* 3.5 34.5 - - + +
58A VAL* 3.7 17.3 - - + +
65A ALA* 3.6 19.7 - - + +
66A SER* 4.2 2.0 - - - -
67A TRP* 3.4 44.3 - - + +
108A VAL* 3.0 24.4 + - + +
109A LEU* 3.2 12.6 - - - +
111A ALA* 1.3 74.7 - - - +
113A ALA* 1.3 60.4 + - - +
115A ARG* 3.3 1.6 + - - -
116A LEU* 2.9 28.9 + - - +
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Residues in contact with ALA 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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67A TRP* 3.9 9.6 - - - -
109A LEU 2.9 12.7 + - - +
110A SER 3.1 8.2 + - - +
112A LEU* 1.3 75.1 - - - +
114A ARG* 1.3 57.5 + - - +
116A LEU* 3.2 6.0 - - - +
117A LEU* 2.9 24.4 + - - +
155A LEU* 3.3 38.5 - - + +
156A TRP* 3.8 11.9 - - - -
157A VAL* 4.1 0.9 - - + -
163A PHE* 3.7 14.1 - - + -
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Residues in contact with ARG 114 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A SER* 2.9 18.0 + - - +
111A ALA* 3.4 12.9 - - - +
113A ALA* 1.3 76.6 - - - +
115A ARG* 1.3 57.3 + - - +
117A LEU* 3.2 7.7 + - - +
118A GLN* 2.9 29.3 + - + +
132A LEU* 3.7 26.3 - - + +
154A ASP* 3.0 33.2 + - - +
155A LEU* 3.2 7.8 + - - +
156A TRP* 3.7 25.5 - - - +
3D A 2.9 39.5 + - - -
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Residues in contact with ARG 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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50A ALA 6.5 0.2 - - - -
51A ARG* 3.5 43.7 - - - +
55A GLY 4.0 6.1 - - - -
56A VAL* 3.5 28.7 - - + -
57A THR 3.9 14.1 + - - +
58A VAL* 4.3 9.4 - - + +
111A ALA 2.9 17.3 + - - +
112A LEU 3.7 5.2 - - - +
114A ARG* 1.3 75.4 - - - +
116A LEU* 1.3 57.5 + - - +
118A GLN* 2.9 37.4 + - - +
119A GLU* 2.9 57.5 + - + +
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Residues in contact with LEU 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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56A VAL* 3.8 24.7 - - + +
67A TRP* 4.6 14.8 - - + -
112A LEU 2.9 14.1 + - - +
113A ALA* 3.2 13.9 - - - +
115A ARG* 1.3 75.2 - - - +
117A LEU* 1.3 66.4 + - - +
119A GLU* 3.1 4.7 + - + +
120A ARG* 2.9 75.7 + - + +
155A LEU* 4.8 4.0 - - + -
163A PHE* 5.6 2.2 - - + -
301A LEU* 4.9 5.2 - - + -
303A LEU* 4.5 17.5 - - + -
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Residues in contact with LEU 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 ALA 2.9 12.3 + - - +
114A ARG* 3.2 8.0 + - - +
116A LEU* 1.3 82.0 - - - +
118A GLN* 1.3 57.2 + - - +
120A ARG* 3.8 1.1 - - - +
121A LEU* 2.9 53.8 + - + +
132A LEU* 3.9 18.4 - - + -
153A LEU* 3.9 15.9 - - + -
154A ASP* 3.8 22.2 - - - -
155A LEU* 3.7 26.9 - - + +
165A LEU* 5.4 2.7 - - + -
297A ILE* 4.4 9.9 - - + -
301A LEU* 4.1 26.7 - - + -
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Residues in contact with GLN 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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51A ARG* 4.3 15.6 + - - +
114A ARG* 2.9 17.4 + - - +
115A ARG* 2.9 42.8 + - - +
117A LEU* 1.3 76.1 - - - +
119A GLU* 1.3 60.6 + - - +
121A LEU* 3.3 6.8 + - - +
122A ARG* 2.9 29.1 + - + +
131A GLY* 4.6 22.7 - - - +
132A LEU* 3.8 17.3 - - + +
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Residues in contact with GLU 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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55A GLY* 4.2 12.9 + - - +
56A VAL* 4.4 14.1 - - + -
115A ARG* 2.9 56.3 + - + +
116A LEU* 3.1 5.8 + - + +
118A GLN* 1.3 78.7 - - - +
120A ARG* 1.3 63.9 + - + +
122A ARG* 3.2 18.8 + - - +
123A ARG* 3.2 14.0 + - - +
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Residues in contact with ARG 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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116A LEU* 2.9 56.1 + - + +
117A LEU 4.2 2.5 - - - +
119A GLU* 1.3 76.4 - - + +
121A LEU* 1.3 65.3 + - - +
123A ARG* 3.4 15.7 + - + +
124A LEU* 3.5 17.4 - - - +
300A ARG 4.6 9.6 - - - +
301A LEU* 2.9 45.3 + - + -
302A GLY 5.5 0.2 + - - -
303A LEU* 4.5 10.1 - - - +
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Residues in contact with LEU 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 LEU* 2.9 40.2 + - + +
118A GLN* 3.6 4.9 - - - +
119A GLU 3.2 0.2 - - - -
120A ARG* 1.3 78.4 - - - +
122A ARG* 1.3 62.3 + - - +
124A LEU* 3.2 26.6 + - + +
129A VAL* 3.8 23.3 - - + +
131A GLY 3.8 18.8 - - - +
132A LEU* 3.9 24.0 - - + +
133A ALA 4.5 0.2 - - - +
134A VAL* 3.5 25.6 - - + -
153A LEU* 4.1 5.6 - - + -
297A ILE* 3.5 31.6 - - + -
301A LEU* 5.9 0.2 - - + -
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Residues in contact with ARG 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 GLN* 2.9 19.5 + - + +
119A GLU* 3.2 14.8 + - - +
121A LEU* 1.3 77.0 - - - +
123A ARG* 1.3 57.2 + - - +
124A LEU 3.2 9.1 + - - +
129A VAL* 4.9 7.4 - - - +
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Residues in contact with ARG 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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119A GLU 3.2 13.0 + - - +
120A ARG* 3.9 12.3 - - + +
121A LEU 3.2 1.4 - - - -
122A ARG* 1.3 76.0 - - - +
124A LEU* 1.3 60.3 + - - +
125A GLU 4.2 0.3 + - - -
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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