Contacts of the helix formed by residues 66 - 80 (chain A) in PDB entry 3NIA
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 PHE 66 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62A MET* 3.8 28.9 - - + -
63A CYS 3.2 21.2 + - - +
64A SER 3.0 1.2 - - - -
65A THR* 1.3 81.2 + - - +
67A LYS* 1.3 68.4 + - + +
68A PHE 3.1 1.0 + - - -
69A PRO* 3.3 12.4 - - - +
70A LEU* 2.9 43.7 + - + -
130A THR* 3.5 33.0 - - + -
134A LEU* 4.1 9.0 - - + -
143A MET* 4.0 21.3 - - + -
147A PHE* 4.9 2.2 - - + -
157A LEU* 3.7 27.6 - - + -
161A GLU* 3.8 3.6 - - - -
164A MET* 3.4 25.4 - - + -
181A MET* 5.1 0.4 - - - -
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Residues in contact with LYS 67 (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 SER* 3.1 29.9 + - - +
65A THR 3.0 1.0 - - - -
66A PHE* 1.3 88.9 - - + +
68A PHE* 1.3 56.6 + - - +
70A LEU* 3.6 10.3 - - + +
71A ALA* 3.0 27.4 + - - +
121A ALA* 3.4 25.9 - - + +
122A VAL* 4.0 5.8 - - - +
125A SER* 2.7 44.5 + - - +
127A ASN* 2.8 16.4 + - - -
130A THR* 3.2 27.3 + - + +
161A GLU* 3.2 16.6 - - - -
229A LYS* 3.8 8.7 - - + -
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Residues in contact with PHE 68 (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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65A THR 3.3 7.1 + - - +
66A PHE 3.1 0.2 - - - -
67A LYS* 1.3 75.3 - - - +
69A PRO* 1.3 74.3 - - + +
71A ALA* 3.0 7.7 + - - +
72A ALA* 3.0 16.8 + - - +
122A VAL* 4.8 4.9 - - - -
185A VAL* 3.7 31.2 - - + -
188A VAL* 4.0 17.3 - - + -
189A LEU* 3.9 22.4 - - + -
202A ILE* 3.5 26.7 - - + -
206A LEU* 3.6 37.0 - - + -
229A LYS* 4.0 16.1 - - + +
241A ILE* 3.9 23.3 - - + -
242A GLY* 4.5 6.3 - - - -
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Residues in contact with PRO 69 (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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65A THR 3.3 9.6 - - - +
66A PHE* 3.3 11.2 - - - +
68A PHE* 1.3 101.6 - - + +
70A LEU* 1.3 55.9 + - - +
72A ALA* 3.1 10.4 + - + +
73A LEU* 2.9 24.6 + - - +
143A MET* 3.7 13.4 - - + +
146A TYR* 4.0 4.9 - - + -
147A PHE* 3.7 37.0 - - + -
181A MET* 4.0 17.0 - - - -
184A THR* 4.4 10.8 - - + -
185A VAL* 6.2 0.4 - - + -
188A VAL* 5.7 2.0 - - + -
241A ILE* 4.4 2.9 - - + -
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Residues in contact with LEU 70 (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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66A PHE* 2.9 27.2 + - + +
67A LYS* 3.6 12.3 - - + +
68A PHE 3.2 0.2 - - - -
69A PRO* 1.3 71.4 - - - +
71A ALA* 1.3 64.5 + - - +
73A LEU* 3.2 5.7 + - + +
74A VAL* 3.0 29.1 + - + +
121A ALA* 5.4 2.0 - - + -
130A THR* 4.0 39.0 - - + +
133A LEU* 4.1 23.3 - - + -
134A LEU* 4.0 14.8 - - + -
137A ILE* 4.0 28.5 - - + -
143A MET* 3.6 18.7 - - - -
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Residues in contact with ALA 71 (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 LYS 3.0 14.6 + - - +
68A PHE 3.0 8.0 + - - +
70A LEU* 1.3 75.7 - - - +
72A ALA* 1.3 57.3 + - - +
74A VAL* 3.2 9.1 + - - +
75A PHE* 2.9 41.9 + - + -
118A ALA* 4.8 7.4 - - + +
122A VAL* 3.7 22.0 - - + -
133A LEU* 6.0 0.9 - - - -
202A ILE* 3.8 14.4 - - + -
205A TRP* 4.7 7.4 - - + -
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Residues in contact with ALA 72 (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 PHE 3.0 12.6 + - - +
69A PRO* 3.1 10.3 + - + +
71A ALA* 1.3 76.4 - - - +
73A LEU* 1.3 56.8 + - - +
75A PHE 3.2 0.9 + - - -
76A GLU* 2.8 27.0 + - - +
146A TYR* 3.7 18.4 - - + +
188A VAL* 3.8 33.7 - - + -
194A LEU* 3.5 19.0 - - + +
202A ILE* 3.9 3.5 - - + +
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Residues in contact with LEU 73 (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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69A PRO 2.9 12.5 + - - +
70A LEU* 3.4 9.9 - - + +
72A ALA* 1.3 76.3 - - - +
74A VAL* 1.3 63.8 + - - +
76A GLU* 3.2 4.5 + - - +
77A ARG* 3.1 44.4 + - - +
137A ILE* 3.8 37.5 - - + -
142A ALA* 3.6 24.9 - - + +
143A MET* 3.7 19.5 - - + -
146A TYR* 3.7 35.1 - - + -
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Residues in contact with VAL 74 (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* 3.0 26.8 + - + +
71A ALA* 3.5 11.0 - - - +
73A LEU* 1.3 78.1 - - - +
75A PHE* 1.3 61.7 + - + +
77A ARG* 3.1 8.3 + - - +
78A ILE* 2.9 34.4 + - + +
83A GLU* 4.6 4.0 - - + +
114A VAL* 3.5 31.4 - - + -
115A LEU* 6.0 0.7 - - + -
118A ALA* 4.9 8.7 - - + -
133A LEU* 4.2 20.9 - - + -
137A ILE* 4.1 22.0 - - + -
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Residues in contact with PHE 75 (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 ALA* 2.9 32.1 + - + +
72A ALA 3.9 3.4 - - - +
74A VAL* 1.3 76.1 - - + +
76A GLU* 1.3 55.3 + - - +
78A ILE* 3.2 17.4 + - + +
79A ASP* 2.7 40.8 + - - +
115A LEU* 3.9 20.9 - - + -
118A ALA* 5.1 2.9 - - + -
194A LEU* 4.2 7.9 - - + -
198A SER* 3.4 36.6 - - - -
201A THR* 3.7 25.8 - - + -
202A ILE* 4.7 12.1 - - + -
205A TRP* 3.5 42.4 - + - -
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Residues in contact with GLU 76 (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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72A ALA 2.8 14.2 + - - +
73A LEU 3.2 9.1 + - - +
75A PHE* 1.3 76.4 - - - +
77A ARG* 1.3 69.9 + - - +
79A ASP* 3.3 6.7 + - + +
80A SER* 2.7 54.5 + - - -
82A THR* 5.5 0.2 + - - -
146A TYR* 4.0 23.1 - - + -
149A LYS* 4.6 20.4 + - + +
193A ALA 4.5 13.7 - - - +
194A LEU* 3.6 11.1 - - + +
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Residues in contact with ARG 77 (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 LEU* 3.1 30.3 + - + +
74A VAL* 3.1 7.4 + - - +
76A GLU* 1.3 83.6 - - - +
78A ILE* 1.3 63.9 + - - +
80A SER* 3.2 1.6 + - - +
81A GLY 3.0 3.8 + - - -
82A THR* 2.9 49.7 + - - +
83A GLU* 3.3 19.5 + - + -
136A GLU 4.5 3.0 + - - -
137A ILE* 2.8 52.8 + - - +
142A ALA* 3.9 13.1 + - - +
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Residues in contact with ILE 78 (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 VAL* 2.9 32.0 + - + +
75A PHE* 3.2 27.1 + - + +
77A ARG* 1.3 76.6 - - - +
79A ASP* 1.3 65.7 + - - +
81A GLY* 3.2 12.1 + - - -
83A GLU* 3.5 27.2 - - + +
84A ARG* 4.4 0.9 - - - -
85A GLY* 3.9 31.4 - - - +
114A VAL* 4.5 1.3 - - + -
115A LEU* 4.3 10.3 - - + -
198A SER* 5.2 1.1 - - - +
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Residues in contact with ASP 79 (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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75A PHE 2.7 24.3 + - - +
76A GLU* 3.4 7.9 - - + +
77A ARG 3.2 0.2 - - - -
78A ILE* 1.3 75.6 - - - +
80A SER* 1.3 61.5 + - - +
81A GLY 3.5 0.5 + - - -
193A ALA 4.8 0.5 - - - +
194A LEU* 3.6 14.2 - - - +
195A THR* 3.0 48.4 + - + +
198A SER* 2.7 23.3 + - - -
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Residues in contact with SER 80 (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 GLU* 2.7 36.7 + - - -
77A ARG* 3.8 4.9 - - - -
78A ILE 3.2 0.4 - - - -
79A ASP* 1.3 77.0 - - - +
81A GLY* 1.3 60.6 + - - +
82A THR* 3.5 18.1 + - - +
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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