Contacts of the helix formed by residues 99 - 115 (chain A) in PDB entry 5NC5
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 99 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97A GLY 3.3 4.7 + - - -
98A THR* 1.3 82.0 - - - +
100A ALA* 1.3 69.4 + - - +
101A ASP* 3.8 19.9 - - - +
102A ILE* 3.3 31.6 + - + +
103A ALA* 3.1 17.5 + - - +
102B ILE* 5.5 1.2 - - - +
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Residues in contact with ALA 100 (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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41A PRO* 4.3 11.2 - - + -
43A VAL* 4.9 1.8 - - + +
98A THR 3.2 4.6 + - - +
99A ASP* 1.3 78.5 + - - +
101A ASP* 1.3 66.0 + - - +
103A ALA* 3.6 7.5 + - - +
104A GLN* 3.3 16.1 + - - +
131A LYS* 3.5 23.4 - - + +
295A THR* 3.9 36.1 - - + +
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Residues in contact with ASP 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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99A ASP* 3.2 19.3 - - - +
100A ALA* 1.3 83.6 + - - +
102A ILE* 1.3 58.2 - - - +
104A GLN* 3.6 9.0 + - - +
105A VAL* 3.0 27.4 + - - +
131A LYS* 4.0 10.5 + - - +
73B ASP* 3.4 17.9 - - - +
102B ILE* 4.3 23.2 - - + +
106B GLN* 3.2 26.8 + - - +
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Residues in contact with ILE 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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98A THR* 6.3 0.9 - - + -
99A ASP* 3.3 30.3 - - + +
100A ALA 3.2 0.2 - - - -
101A ASP* 1.3 76.5 - - - +
103A ALA* 1.3 64.8 + - - +
104A GLN 3.0 1.3 - - - -
105A VAL* 3.5 7.5 - - + -
106A GLN* 2.9 45.5 + - + +
102B ILE* 4.2 21.8 - - + -
101C ASP* 4.2 33.7 - - + +
102C ILE* 5.9 2.7 - - + -
105C VAL* 4.2 18.4 - - + -
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Residues in contact with ALA 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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41A PRO* 5.8 2.0 - - + -
43A VAL* 4.1 7.9 - - + -
94A PHE* 3.6 45.5 - - + -
98A THR* 4.5 5.3 - - + +
99A ASP 3.1 17.2 + - - +
100A ALA* 3.6 6.9 + - - +
102A ILE* 1.3 75.7 - - - +
104A GLN* 1.3 58.3 + - - +
106A GLN* 3.4 6.0 + - - +
107A VAL* 3.0 33.4 + - - +
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Residues in contact with GLN 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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43A VAL* 4.1 13.0 - - + -
100A ALA 3.3 10.8 + - - +
101A ASP 3.6 9.1 - - - +
102A ILE 3.0 0.6 - - - -
103A ALA* 1.3 79.9 - - - +
105A VAL* 1.3 66.6 + - - +
107A VAL* 4.0 2.7 - - - +
108A GLN* 2.9 30.2 + - - +
129A VAL* 3.2 39.2 + - + +
130A GLU* 4.4 6.1 - - - +
131A LYS* 4.0 21.5 - - + +
71B GLY 5.2 4.8 + - - -
106B GLN* 4.0 27.0 + - - +
109B ASN* 5.4 4.7 + - - +
110B LYS* 3.8 16.0 - - - +
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Residues in contact with VAL 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 ASP 3.0 20.0 - - - +
102A ILE* 3.0 20.1 + - + +
104A GLN* 1.3 79.7 - - + +
106A GLN* 1.3 54.8 + - + +
108A GLN* 3.7 1.2 - - - +
109A ASN* 2.8 32.6 + - - +
102B ILE* 5.3 2.0 - - + -
105B VAL* 4.0 33.2 - - + -
106B GLN* 6.1 1.8 - - + -
109B ASN* 4.1 10.7 + - - +
104C GLN* 4.3 11.7 - - - +
105C VAL* 4.3 4.7 - - + -
108C GLN* 3.7 29.8 + - - +
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Residues in contact with GLN 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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71A GLY 5.0 4.3 - - - +
72A ILE* 3.6 18.5 - - + +
73A ASP* 2.9 55.5 + - - +
102A ILE* 2.9 28.3 + - + +
103A ALA* 3.9 5.6 - - - +
105A VAL* 1.3 76.8 - - + +
107A VAL* 1.3 66.1 + - - +
109A ASN* 3.1 16.7 + - - +
110A LYS* 3.2 15.4 + - - +
101C ASP* 3.7 15.8 + - - -
104C GLN* 6.2 5.2 - - + +
131C LYS* 4.7 4.4 - - - +
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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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43A VAL* 4.2 16.8 - - + -
45A ILE* 3.4 36.3 - - + -
69A MET* 3.7 6.4 - - - +
72A ILE* 4.3 13.5 - - + -
92A LEU* 4.2 18.8 - - + -
94A PHE* 4.0 21.1 - - + -
103A ALA 3.0 22.1 + - - +
104A GLN 4.0 2.7 - - - +
106A GLN* 1.3 75.2 - - - +
108A GLN* 1.3 67.2 + - - +
110A LYS* 3.0 6.1 + - - +
111A LEU* 2.9 18.9 + - - +
129A VAL* 4.5 3.8 - - + -
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Residues in contact with GLN 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 GLN* 2.9 24.4 + - - +
105A VAL 4.0 2.2 - - - +
107A VAL* 1.3 80.0 - - - +
109A ASN* 1.3 62.8 + - - +
111A LEU* 4.2 11.0 - - + -
112A GLN* 3.0 24.6 + - + +
129A VAL* 3.7 25.8 - - + +
109B ASN* 3.0 54.4 + - - +
110B LYS* 4.6 5.4 + - - -
112B GLN* 4.1 12.7 + - - +
113B LEU* 3.2 32.5 - - - +
108C GLN* 5.6 0.4 - - - -
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Residues in contact with ASN 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 VAL 2.8 16.0 + - - +
106A GLN* 3.1 11.8 + - - +
108A GLN* 1.3 76.4 - - - +
110A LYS* 1.3 75.4 + - - +
112A GLN* 2.9 45.4 + - - +
113A LEU* 3.4 5.4 - - - +
112B GLN* 6.2 0.2 - - - +
104C GLN* 5.0 1.6 - - - +
108C GLN* 4.1 24.4 + - - +
127C VAL 4.6 0.2 - - - +
128C SER* 4.5 4.8 - - - -
129C VAL* 3.3 42.1 + - - +
130C GLU* 4.2 7.3 + - - -
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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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68A ASN* 3.4 29.6 - - - +
69A MET* 3.6 15.3 - - + -
70A ASN* 2.8 42.1 + - - +
71A GLY 4.4 3.8 - - - -
72A ILE* 4.4 7.6 - - + -
106A GLN 3.2 10.3 + - - +
107A VAL 3.0 4.0 + - - +
109A ASN* 1.3 84.6 - - - +
111A LEU* 1.3 67.8 + - - +
113A LEU* 3.0 34.8 + - + +
114A ALA 3.7 2.3 + - - -
128C SER* 5.5 2.0 - - - -
130C GLU* 2.8 39.7 + - - -
174C ASP* 5.9 0.6 + - - -
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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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45A ILE* 3.8 17.3 - - + -
65A ILE* 3.6 37.0 - - + -
69A MET* 3.5 11.5 - - + +
107A VAL 2.9 15.5 + - - +
108A GLN* 3.1 10.1 + - + +
110A LYS* 1.3 77.2 - - - +
112A GLN* 1.3 56.0 + - - +
114A ALA* 2.9 24.7 + - + +
115A MET* 2.9 24.8 + - + -
118A LEU* 5.3 0.4 - - + -
127A VAL* 4.5 9.0 - - + -
129A VAL* 3.5 29.4 - - + -
113B LEU* 4.1 21.3 - - + -
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Residues in contact with GLN 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 GLN* 3.0 15.0 + - + +
109A ASN* 2.9 37.1 + - - +
111A LEU* 1.3 75.7 - - + +
113A LEU* 1.3 70.3 + - - +
114A ALA 3.3 0.2 - - - -
115A MET* 3.8 15.0 - - + +
116A PRO* 3.2 17.8 - - - +
112B GLN* 3.2 34.1 - - + +
113B LEU* 6.3 0.7 - - + -
108C GLN* 6.2 0.2 - - - +
115C MET* 5.5 6.8 - - - +
126C GLY* 4.8 4.0 - - - -
127C VAL 3.1 32.6 + - - +
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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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68A ASN* 3.7 18.6 - - + +
109A ASN 3.4 6.3 - - - +
110A LYS* 3.0 30.3 + - + +
112A GLN* 1.3 111.9 - - - +
114A ALA* 1.3 58.2 + - - +
116A PRO* 3.4 14.9 - - - +
117A LEU* 4.6 6.6 - - - +
125C GLN 4.4 10.8 - - - +
126C GLY* 4.7 11.0 - - - -
127C VAL 4.2 3.8 - - - +
128C SER* 4.1 32.1 - - - +
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Residues in contact with ALA 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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64A VAL* 3.6 31.4 - - + +
65A ILE* 4.1 18.8 - - + -
68A ASN* 3.6 15.5 + - + +
110A LYS 3.7 0.6 + - - -
111A LEU* 2.9 10.6 + - + +
113A LEU* 1.3 76.9 - - - +
115A MET* 1.3 65.2 + - - +
116A PRO* 3.2 3.4 - - - -
117A LEU* 2.8 21.0 + - - +
118A LEU* 3.5 11.4 + - + +
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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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111A LEU* 2.9 30.5 + - + +
112A GLN* 3.8 16.4 - - + +
114A ALA* 1.3 77.1 - - - +
116A PRO* 1.3 69.6 - - + +
118A LEU* 3.1 28.5 + - - +
123A GLN* 3.4 42.7 + - + +
127A VAL* 3.9 32.3 - - + +
112B GLN 5.5 2.0 - - - +
113B LEU* 4.9 16.6 - - + +
116B PRO* 4.4 16.8 - - + -
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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