Contacts of the helix formed by residues 100 - 118 (chain A) in PDB entry 3N1Q
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 THR 100 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76A ASP 5.2 3.4 - - - -
77A LEU* 3.8 13.9 - - + -
99A MET* 1.3 79.0 - - - +
101A GLU* 1.3 62.5 + - - +
103A CYS* 3.3 18.7 + - - +
104A LYS* 3.3 21.5 + - - +
143A GLU 3.8 8.3 - - - +
144A GLY 3.2 13.4 + - - +
145A ARG* 3.6 20.0 - - + +
186A VAL* 3.9 9.2 - - - +
189A ASP* 2.8 27.5 + - + +
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Residues in contact with GLU 101 (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 ASP 4.7 8.0 + - - +
78A VAL* 3.6 29.5 + - - +
100A THR* 1.3 73.8 - - - +
102A ARG* 1.3 67.9 + - - +
104A LYS* 3.1 28.2 + - - +
105A GLU* 3.2 20.1 + - - +
189A ASP* 3.1 13.0 + - + +
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Residues in contact with ARG 102 (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 THR* 4.3 1.1 - - - +
101A GLU* 1.3 77.8 - - - +
103A CYS* 1.3 62.7 + - - +
105A GLU* 3.5 11.9 + - - +
106A ARG* 3.1 63.2 + - - +
170A GLY 4.8 0.8 + - - -
172A ASP* 2.9 38.1 + - - -
186A VAL* 4.2 6.1 - - + -
187A LYS* 3.7 38.9 - - - +
188A ALA 4.5 5.2 - - - -
189A ASP* 3.0 23.6 + - - +
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Residues in contact with CYS 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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99A MET* 4.0 19.7 - - + -
100A THR* 3.3 23.0 + - - +
102A ARG* 1.3 79.1 - - - +
104A LYS* 1.3 58.3 + - - +
106A ARG* 2.9 6.2 + - - +
107A VAL* 2.8 31.8 + - - +
144A GLY 4.4 6.3 - - - +
145A ARG 4.7 6.1 - - - -
147A LEU* 3.7 36.3 - - - -
171A PHE* 4.6 5.6 - - - -
186A VAL* 3.9 20.7 - - + +
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Residues in contact with LYS 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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78A VAL* 3.0 54.9 + - - +
79A PRO 3.1 20.6 + - - -
80A ASN* 3.8 14.8 - - + +
99A MET* 3.5 25.5 - - + -
100A THR 3.3 5.8 + - - +
101A GLU* 3.1 24.0 + - - +
103A CYS* 1.3 79.5 - - - +
105A GLU* 1.3 56.4 + - + +
106A ARG 3.0 0.2 + - - -
107A VAL* 4.1 1.6 - - - -
108A ASN* 2.8 51.8 + - - +
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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
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101A GLU* 3.2 14.9 + - + +
102A ARG* 3.6 9.9 - - - +
103A CYS 3.3 0.2 + - - -
104A LYS* 1.3 78.3 - - + +
106A ARG* 1.3 87.6 + - - +
108A ASN* 4.2 5.3 - - - +
109A ALA* 3.4 22.5 + - - +
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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
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102A ARG* 3.1 59.2 + - - +
103A CYS 2.9 7.0 + - - +
105A GLU* 1.3 116.2 + - - +
107A VAL* 1.3 61.2 + - - +
109A ALA* 3.2 3.5 + - - +
110A LEU* 2.9 29.5 + - - +
169A ALA* 3.5 14.2 - - - +
170A GLY* 2.7 36.9 + - - +
171A PHE* 3.4 25.5 - - + -
172A ASP* 5.3 0.2 + - - -
186A VAL* 4.0 14.1 - - + -
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Residues in contact with VAL 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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80A ASN* 4.4 8.1 - - - +
85A ILE* 3.6 14.4 - - + -
87A PHE* 5.7 0.7 - - + -
99A MET* 4.0 9.4 - - + -
103A CYS* 2.8 29.5 + - - +
104A LYS 3.9 1.6 - - - +
106A ARG* 1.3 72.0 - - - +
108A ASN* 1.3 53.1 + - - +
110A LEU* 3.1 3.3 + - - +
111A ALA* 2.7 36.2 + - - +
123A LEU* 3.6 23.2 - - + +
125A VAL* 4.7 5.8 - - + -
147A LEU* 3.3 35.2 - - + -
149A ILE* 5.9 0.4 - - + -
171A PHE* 3.8 12.1 - - + -
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Residues in contact with ASN 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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80A ASN* 3.0 26.1 + - - +
82A ASN* 3.2 26.8 + - - +
85A ILE* 4.4 0.2 - - - +
104A LYS* 2.8 39.7 + - - +
105A GLU* 4.2 6.0 - - - +
107A VAL* 1.3 73.1 - - - +
109A ALA* 1.3 59.5 + - - +
111A ALA* 3.5 3.7 + - - +
112A ILE* 3.3 27.0 + - - +
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Residues in contact with ALA 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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105A GLU 3.4 17.1 + - - +
106A ARG 3.2 5.1 + - - +
107A VAL 3.2 0.4 - - - -
108A ASN* 1.3 75.5 - - - +
110A LEU* 1.3 67.3 + - - +
112A ILE* 3.2 14.3 + - - +
113A ALA* 3.0 20.3 + - - +
169A ALA* 4.0 20.2 - - + +
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Residues in contact with LEU 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 17.2 + - - +
107A VAL* 3.5 4.3 - - + +
109A ALA* 1.3 73.1 - - - +
111A ALA* 1.3 56.7 + - - +
113A ALA* 3.0 6.2 + - + +
114A VAL* 2.8 44.8 + - + +
123A LEU* 3.8 20.4 - - + -
149A ILE* 3.6 31.6 - - + -
162A LEU* 4.4 3.6 - - + +
165A LEU* 3.4 45.1 - - + +
166A ALA* 3.6 6.1 - - + +
169A ALA* 3.8 8.5 - - + +
171A PHE* 3.9 19.7 - - + -
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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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82A ASN* 4.4 5.4 - - - +
84A ASP* 4.2 12.5 - - + +
85A ILE* 3.7 29.6 - - + -
107A VAL 2.7 19.5 + - - +
108A ASN* 3.5 8.7 - - - +
109A ALA 3.3 0.2 - - - -
110A LEU* 1.3 72.7 - - - +
112A ILE* 1.3 61.6 + - + +
114A VAL* 3.5 2.0 + - - +
115A MET* 3.1 31.1 + - - +
123A LEU* 4.2 13.6 + - + +
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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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108A ASN 3.3 13.2 + - - +
109A ALA* 3.2 13.4 + - - +
110A LEU 3.1 0.6 - - - -
111A ALA* 1.3 77.7 - - + +
113A ALA* 1.3 65.4 + - - +
115A MET* 3.5 6.8 + - - +
116A ASN* 3.2 23.8 + - + +
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Residues in contact with ALA 113 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A ALA 3.0 11.5 + - - +
110A LEU* 3.0 17.1 + - + +
112A ILE* 1.3 78.2 - - - +
114A VAL* 1.3 57.7 + - - +
116A ASN* 3.4 9.6 + - - +
117A MET* 2.9 30.7 + - - +
165A LEU* 3.8 27.2 - - + +
169A ALA* 5.8 1.8 - - + -
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Residues in contact with VAL 114 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110A LEU* 2.8 26.0 + - + +
111A ALA 3.8 5.2 - - - +
112A ILE 3.2 0.2 - - - -
113A ALA* 1.3 74.1 - - - +
115A MET* 1.3 66.7 + - - +
117A MET* 3.1 2.9 + - - +
118A TRP* 3.0 33.0 + - + +
121A VAL* 4.1 9.0 - - + -
122A ARG* 3.6 37.0 - - - +
123A LEU* 4.0 17.9 - - + +
151A THR* 5.4 1.8 - - + -
162A LEU* 3.7 28.9 - - + -
165A LEU* 4.5 5.8 - - + -
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Residues in contact with MET 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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84A ASP* 3.3 43.3 - - + +
111A ALA 3.1 17.7 + - - +
112A ILE* 4.1 6.3 - - - +
113A ALA 3.5 0.2 - - - -
114A VAL* 1.3 75.8 - - - +
116A ASN* 1.3 61.4 + - - +
118A TRP 3.4 16.4 - - - +
119A PRO* 3.7 8.1 - - - +
120A GLY* 4.8 5.6 + - - +
121A VAL 3.7 20.2 - - - +
122A ARG* 3.8 26.5 - - + +
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Residues in contact with ASN 116 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112A ILE* 3.2 20.2 + - + +
113A ALA* 3.6 9.7 + - - +
114A VAL 3.1 0.2 - - - -
115A MET* 1.3 78.8 - - - +
117A MET* 1.3 67.8 + - - +
118A TRP* 4.7 0.2 - - - -
119A PRO* 4.7 6.1 - - - +
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Residues in contact with MET 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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40A LEU* 3.5 30.7 - - + -
113A ALA 2.9 16.8 + - - +
114A VAL 3.1 4.0 + - - +
116A ASN* 1.3 83.3 - - - +
118A TRP* 1.3 97.5 + - + +
119A PRO* 3.8 6.0 - - - +
161A LEU* 3.5 20.2 - - + -
165A LEU* 3.9 26.0 - - + -
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Residues in contact with TRP 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 VAL* 3.0 32.6 + - + +
115A MET 3.4 8.2 - - - +
117A MET* 1.3 109.4 - - + +
119A PRO* 1.3 65.3 - - + +
120A GLY 3.3 0.2 + - - -
121A VAL* 2.9 43.4 + - + +
151A THR* 4.0 16.8 - - + -
158A LYS* 3.5 61.4 - - + +
161A LEU* 3.5 22.9 - - + +
162A LEU* 4.0 24.7 - - + -
165A LEU* 4.4 6.7 - - + -
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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