Contacts of the helix formed by residues 99 - 105 (chain C) in PDB entry 3DLX
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 LEU 99 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61C VAL* 3.6 37.7 - - + -
69C ILE* 5.6 2.0 - - - +
74C ILE* 4.1 3.1 - - + +
87C ALA* 4.0 3.4 - - + -
89C SER* 3.5 23.8 - - - +
91C ASN 4.1 0.4 - - - +
92C ALA* 4.1 12.3 - - - -
93C GLY* 4.3 5.3 - - - +
97C PHE 3.8 0.4 + - - -
98C GLY* 1.3 69.3 - - - -
100C GLY* 1.3 62.4 + - - +
101C LEU 3.1 0.4 - - - -
102C LEU* 2.9 27.2 + - + +
103C LEU* 3.1 14.9 + - + +
108C ILE* 3.8 17.3 - - + -
111C MET* 2.9 49.8 - - + -
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Residues in contact with GLY 100 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA 3.5 5.4 + - - -
94C VAL 3.2 21.1 - - - -
95C ASP 3.6 7.6 - - - -
97C PHE 3.4 3.0 + - - -
98C GLY 3.0 2.6 + - - -
99C LEU* 1.3 78.0 - - - +
101C LEU* 1.3 56.4 + - - +
103C LEU* 3.5 6.7 + - - +
104C ARG* 2.9 33.8 + - - +
119C ASN* 3.6 15.3 - - - -
121C GLU* 5.5 0.7 - - - +
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Residues in contact with LEU 101 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71C GLU 5.9 1.8 - - - +
74C ILE* 4.3 13.5 - - + -
75C ASP* 5.7 3.8 - - + +
78C LEU* 3.5 32.6 - - + +
95C ASP 4.1 0.9 + - - +
96C ASN* 3.6 35.0 - - + +
97C PHE* 4.2 11.0 + - + -
98C GLY 3.1 18.3 + - - +
100C GLY* 1.3 78.8 - - - +
102C LEU* 1.3 59.8 + - - +
104C ARG* 3.6 9.0 + - + +
105C SER* 3.4 20.1 + - - -
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Residues in contact with LEU 102 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61C VAL* 5.9 2.5 - - + -
74C ILE* 3.7 32.8 - - + +
77C LEU* 3.8 40.4 - - + -
78C LEU* 3.7 20.6 - - + -
85C LEU* 5.5 4.3 - - + -
99C LEU* 2.9 23.2 + - + +
101C LEU* 1.3 74.8 - - - +
103C LEU* 1.3 62.3 + - - +
104C ARG 3.4 0.2 - - - -
105C SER* 3.4 3.2 + - - -
106C LYS 3.2 2.6 + - - -
107C GLN* 2.9 46.6 + - + +
108C ILE* 3.8 21.1 + - + -
209C LEU* 5.8 0.4 - - + -
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Residues in contact with LEU 103 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92C ALA* 4.1 15.0 - - + +
99C LEU 3.1 17.7 + - - +
100C GLY* 3.5 6.0 + - - +
102C LEU* 1.3 75.6 - - - +
104C ARG* 1.3 61.5 + - - +
105C SER 3.2 0.4 - - - -
106C LYS* 3.1 10.8 + - - +
107C GLN 5.0 0.2 - - - +
108C ILE* 3.8 24.7 - - + +
111C MET* 4.3 6.7 - - + -
119C ASN* 4.3 8.3 - - - +
121C GLU* 4.6 6.7 - - + -
122C PHE* 3.8 35.0 - - + -
125C GLN* 2.5 36.2 + - - +
131C LEU* 3.7 37.0 - - + -
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Residues in contact with ARG 104 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95C ASP* 3.5 36.0 + - - +
100C GLY 2.9 29.2 + - - +
101C LEU* 3.9 11.7 - - + +
102C LEU 3.4 0.2 - - - -
103C LEU* 1.3 76.1 - - - +
105C SER* 1.3 59.7 + - - +
106C LYS* 3.2 9.5 + - - +
121C GLU* 3.8 35.5 + - + +
125C GLN* 5.1 0.2 - - - -
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Residues in contact with SER 105 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78C LEU* 3.6 8.8 - - - +
101C LEU 3.4 14.9 + - - -
102C LEU* 3.4 4.3 + - - -
103C LEU 3.2 0.4 - - - -
104C ARG* 1.3 76.3 - - - +
106C LYS* 1.3 71.4 + - - +
107C GLN* 2.4 36.4 + - - +
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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