Contacts of the helix formed by residues 68 - 78 (chain A) in PDB entry 3CX5
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 GLY 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A GLU* 3.0 11.9 + - - -
67A ASN* 1.3 74.6 + - - +
69A VAL* 1.3 58.5 + - - +
70A SER 3.3 2.9 - - - -
71A ASN* 3.2 6.9 + - - +
72A LEU* 2.9 28.9 + - - +
144A VAL* 6.0 0.3 - - - +
178A THR 5.0 1.3 - - - -
179A ARG 3.9 5.4 - - - -
180A GLY* 3.5 12.6 - - - -
185A LEU* 3.4 17.1 - - - +
188A LEU* 4.0 6.5 - - - -
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Residues in contact with VAL 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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62A GLU* 3.5 14.8 - - + +
66A ASN* 3.0 27.9 + - + +
68A GLY* 1.3 78.1 - - - +
70A SER* 1.3 65.4 + - - +
72A LEU* 3.1 5.1 + - - +
73A TRP* 3.0 25.6 + - + -
188A LEU* 3.8 12.9 - - + +
192A ASP* 3.8 14.8 - - + +
193A LEU* 3.9 20.4 - - + -
196A PHE* 3.6 46.0 - - + -
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Residues in contact with SER 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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58A GLY 4.1 4.6 + - - -
62A GLU* 2.9 20.1 + - - -
69A VAL* 1.3 78.8 - - - +
71A ASN* 1.3 57.8 + - - +
73A TRP* 3.1 8.1 + - - +
74A LYS 3.0 24.9 + - - -
97A ILE* 3.3 29.3 - - - +
102A GLN* 3.2 34.8 + - - -
196A PHE* 3.4 15.0 - - - -
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Residues in contact with ASN 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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68A GLY* 3.2 10.6 + - - +
70A SER* 1.3 78.4 - - - +
72A LEU* 1.3 60.6 + - - +
74A LYS* 3.5 13.0 + - - +
75A ASN* 2.9 43.6 + - - -
97A ILE* 3.9 12.0 - - + +
144A VAL* 4.5 14.6 - - + +
147A GLN* 4.5 8.5 + - - +
148A VAL* 4.1 10.5 - - - +
178A THR 3.8 12.9 + - - +
179A ARG* 3.0 42.4 + - - +
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Residues in contact with LEU 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 GLY 2.9 12.1 + - - +
69A VAL* 3.4 10.5 - - - +
70A SER 3.1 0.2 - - - -
71A ASN* 1.3 75.6 - - - +
73A TRP* 1.3 64.5 + - - +
75A ASN* 3.3 3.3 + - - +
76A ILE* 3.1 29.8 + - + +
137A PHE* 3.6 33.4 - - + +
140A THR* 4.2 4.0 - - + -
141A LYS* 3.9 22.2 - - + +
144A VAL* 3.5 38.1 - - + +
185A LEU* 5.4 3.1 - - + +
188A LEU* 3.9 19.5 - - + -
193A LEU* 3.8 20.2 - - + -
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Residues in contact with TRP 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 VAL* 3.0 30.3 + - + +
70A SER* 3.1 8.7 + - - +
72A LEU* 1.3 74.7 - - - +
74A LYS* 1.3 65.9 + - - +
76A ILE* 3.2 37.6 + - + +
77A PHE* 3.1 23.9 + - + +
102A GLN* 4.2 0.7 - - - +
104A TYR* 3.4 17.7 - + - +
124A PHE* 5.6 9.0 - + - -
128A LYS* 4.4 10.5 - - + -
131A LEU* 5.8 1.3 - - + -
132A LEU* 3.9 26.0 - - + -
193A LEU* 2.9 53.9 + - + +
194A GLU 4.2 1.3 - - - -
196A PHE* 4.3 6.1 - + - -
197A ALA* 3.6 16.0 - - + +
201A PHE* 3.9 29.2 - + - -
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Residues in contact with LYS 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 SER 3.0 5.7 + - - -
71A ASN* 3.6 13.7 + - - +
73A TRP* 1.3 76.8 - - - +
75A ASN* 1.3 70.9 + - - +
77A PHE* 3.3 3.5 + - - +
78A LEU* 3.1 44.3 + - + +
95A SER* 3.2 47.7 + - - +
96A ASN* 5.0 5.9 - - - +
97A ILE* 3.7 31.2 - - + +
104A TYR* 3.9 6.4 + - - -
147A GLN* 5.6 3.4 + - - -
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Residues in contact with ASN 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 ASN* 2.9 36.0 + - - +
72A LEU 3.3 1.1 + - - +
73A TRP 3.2 0.8 - - - -
74A LYS* 1.3 89.4 - - - +
76A ILE* 1.3 58.8 + - - +
78A LEU* 3.4 10.3 + - - +
79A SER* 3.0 23.6 + - - -
140A THR* 3.6 23.7 + - + +
143A SER* 4.8 3.7 + - - -
144A VAL* 3.6 17.3 - - + +
147A GLN* 3.4 27.1 + - - +
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Residues in contact with ILE 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 LEU* 3.1 19.9 + - + +
73A TRP* 3.2 46.2 - - + +
75A ASN* 1.3 76.6 - - - +
77A PHE* 1.3 65.4 + - + +
79A SER* 2.9 25.4 - - - -
82A ASN* 4.2 6.2 - - - +
124A PHE* 6.6 0.2 - - + -
131A LEU* 3.7 43.2 - - + +
132A LEU* 4.6 6.3 - - + -
136A ASN* 4.4 8.2 + - - +
137A PHE* 5.1 10.8 - - + -
140A THR* 3.6 22.0 - - + +
193A LEU* 4.8 8.3 - - + -
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Residues in contact with PHE 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 TRP* 3.1 13.2 + - + +
74A LYS 3.4 7.4 - - - +
76A ILE* 1.3 86.2 - - + +
78A LEU* 1.3 65.6 + - + +
79A SER 3.2 0.7 - - - -
82A ASN* 2.9 42.0 + - - +
93A LEU* 3.4 41.0 - - + +
94A SER 3.9 19.3 - - - -
95A SER* 4.1 4.9 - - - -
104A TYR* 3.7 42.8 - + + -
105A ILE 4.2 6.5 - - - -
106A VAL* 4.6 5.6 - - + -
119A PHE* 4.1 11.4 - + - -
120A LEU* 4.9 5.8 - - + -
123A SER* 4.4 14.1 - - - -
124A PHE* 4.5 13.2 - + + -
131A LEU* 5.0 2.0 - - + -
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Residues in contact with LEU 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 LYS* 3.1 46.6 + - + +
75A ASN* 3.4 12.3 + - - +
76A ILE 3.2 0.2 - - - -
77A PHE* 1.3 83.9 - - + +
79A SER* 1.3 65.9 + - - +
80A LYS* 3.7 0.7 + - - -
83A SER* 3.2 12.4 + - - +
93A LEU* 3.6 42.6 - - + +
94A SER* 4.0 6.7 - - - +
95A SER* 4.4 7.9 - - - +
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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