Contacts of the helix formed by residues 61 - 67 (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 VAL 61 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A ALA* 4.0 15.9 - - + -
49A TYR* 4.4 6.3 - - + -
57A VAL* 3.1 11.5 + - - +
59A ASP 3.7 0.2 - - - -
60A THR* 1.3 92.1 - - - +
62A THR* 1.3 71.2 + - - +
63A GLN 3.2 2.2 + - - -
64A VAL* 3.3 3.3 + - - +
65A ILE* 3.2 39.2 + - + +
88A VAL* 3.8 23.3 - - + -
118A LEU* 4.1 11.4 - - + -
119A PRO* 4.1 4.3 - - + -
122A VAL* 3.6 29.6 - - + -
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Residues in contact with THR 62 (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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57A VAL 3.0 11.8 + - - -
58A GLN* 3.1 14.1 + - - -
61A VAL* 1.3 78.0 - - - +
63A GLN* 1.3 57.7 + - - +
65A ILE* 3.4 2.6 + - - +
66A GLU* 3.0 45.2 + - - +
80A SER* 3.7 19.3 - - - +
82A SER* 3.4 17.7 + - - +
88A VAL* 2.9 25.0 - - + +
90A ILE* 4.0 13.2 - - + +
818A ARG* 4.3 6.5 - - - -
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Residues in contact with GLN 63 (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 GLN* 3.0 26.6 + - + +
59A ASP* 3.4 20.2 + - - -
62A THR* 1.3 77.3 - - - +
64A VAL* 1.3 60.3 + - + +
66A GLU* 3.2 7.6 + - - +
67A GLN* 2.9 46.2 + - - +
818A ARG* 3.8 29.7 + - - +
763C ILE* 5.1 0.2 - - - +
766C GLY 3.0 23.4 + - - -
767C ARG* 3.8 6.4 + - - +
768C VAL* 3.3 40.8 + - + +
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Residues in contact with VAL 64 (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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59A ASP 4.6 8.3 - - - +
60A THR* 4.1 20.2 - - - +
61A VAL 3.7 6.3 - - - +
63A GLN* 1.3 79.7 - - + +
65A ILE* 1.3 56.2 + - - +
67A GLN* 3.7 7.7 + - - +
68A ASN* 2.6 33.7 + - - +
114A ALA* 3.6 7.2 - - + +
117A LEU* 4.0 38.1 - - + +
118A LEU* 4.0 15.0 - - + -
761C ASP* 4.8 13.5 - - - +
768C VAL* 4.9 6.3 - - + -
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Residues in contact with ILE 65 (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* 4.2 19.3 - - + -
47A ALA* 5.3 2.2 - - + -
61A VAL* 3.2 26.6 + - + +
64A VAL* 1.3 77.7 - - - +
66A GLU* 1.3 58.6 + - - +
68A ASN* 2.9 20.3 + - - +
69A MET* 3.4 26.2 + - + +
88A VAL* 6.0 0.7 - - + -
90A ILE* 3.8 24.0 - - + -
111A LEU* 3.6 34.1 - - + -
114A ALA* 4.1 9.2 - - + -
118A LEU* 4.0 25.1 - - + -
127A VAL* 5.2 3.4 - - + -
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Residues in contact with GLU 66 (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 THR* 3.0 23.3 + - - +
63A GLN* 3.2 6.3 + - - +
65A ILE* 1.3 77.3 - - - +
67A GLN* 1.3 59.9 + - + +
68A ASN 3.4 0.5 + - - -
69A MET* 3.5 9.1 + - - +
78A MET* 3.6 27.7 - - + +
80A SER* 3.5 25.9 + - - -
90A ILE* 4.2 14.1 - - + -
818A ARG* 3.1 36.2 + - - +
821A GLY* 3.7 28.6 + - - +
164C ASP* 4.2 1.1 - - - +
168C ARG* 3.2 25.1 + - - -
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Residues in contact with GLN 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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63A GLN* 2.9 40.2 + - - +
64A VAL* 4.2 7.6 - - - +
65A ILE 3.1 0.4 - - - -
66A GLU* 1.3 78.4 - - + +
68A ASN* 1.3 63.7 + - - +
69A MET 3.5 0.2 - - - -
70A ASN* 3.7 10.3 + - - -
164C ASP* 3.7 28.3 - - - +
168C ARG* 5.6 0.2 - - - -
181C GLN* 5.3 2.6 + - - +
767C ARG* 3.5 30.8 + - - +
768C VAL* 3.2 32.7 + - - +
770C LYS* 5.9 1.2 + - - -
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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