Contacts of the helix formed by residues 104 - 110 (chain C) in PDB entry 2HU4
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 ASN 104 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137B GLY* 3.4 18.9 - - - +
155B HIS* 2.9 34.8 - - - +
157B THR* 4.2 13.5 + - - +
102C LYS* 2.6 41.5 - - - +
103C ASP* 1.3 81.6 + - - +
105C SER* 1.3 65.2 + - - +
106C ILE 3.1 4.0 + - - -
107C ARG* 3.1 15.7 + - - +
108C ILE* 3.0 32.7 + - + +
442C SER* 4.0 6.0 + - - -
443C SER 4.7 0.2 + - - -
460C ASP 4.0 1.5 + - - -
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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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103C ASP* 2.8 12.2 + - - -
104C ASN* 1.3 75.6 - - - +
106C ILE* 1.3 55.4 + - - +
108C ILE* 3.3 2.0 + - - +
109C GLY* 2.6 33.4 + - - -
114C VAL* 3.8 15.2 - - - +
117C ILE* 5.5 0.2 - - - +
140C LEU* 5.6 0.2 - - - +
166C ALA* 3.9 14.1 - - - -
167C PRO* 3.6 31.6 - - - +
441C GLY 3.3 22.0 + - - -
442C SER* 3.3 7.8 + - - -
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Residues in contact with ILE 106 (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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104C ASN 3.1 0.2 + - - -
105C SER* 1.3 74.5 + - - +
107C ARG* 1.3 66.9 + - - +
109C GLY* 3.2 9.5 + - - -
110C SER 3.4 8.5 + - - -
140C LEU* 4.2 10.3 - - + -
428C ARG* 3.5 24.9 - - + -
438C TRP* 4.5 11.4 - - + -
440C SER* 3.8 13.9 - - - +
441C GLY* 3.7 33.0 - - - +
442C SER* 3.2 9.3 + - - +
460C ASP* 3.3 21.8 - - - +
462C ALA* 3.4 20.6 - - + -
464C LEU* 5.2 0.2 - - + -
466C PHE* 3.6 20.6 - - + -
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Residues in contact with ARG 107 (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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136B GLN* 2.6 28.3 + - - +
137B GLY 2.8 26.4 + - - +
138B ALA* 4.8 2.6 - - - -
139B LEU 5.2 0.5 + - - -
142B ASP* 3.9 3.5 - - - +
144B HIS* 3.4 58.1 + - + +
148B THR* 5.6 1.2 - - - +
150B LYS* 5.9 4.6 - - - +
155B HIS* 3.8 28.5 + - - +
104C ASN* 3.1 15.6 + - - +
106C ILE* 1.3 77.5 - - - +
108C ILE* 1.3 63.3 + - - +
110C SER* 3.5 4.9 - - - -
442C SER* 5.0 0.2 + - - -
460C ASP* 3.1 24.6 + - - +
461C GLY* 2.9 36.9 + - - +
462C ALA* 3.4 7.9 - - - +
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Residues in contact with ILE 108 (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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115B PHE* 3.7 28.5 - - + -
137B GLY* 4.3 9.6 - - - +
138B ALA* 4.7 2.5 - - - +
139B LEU* 3.4 33.6 - - + +
142B ASP* 5.7 0.2 - - - -
169B PRO* 4.4 13.9 - - + -
103C ASP 3.3 26.0 - - - +
104C ASN* 3.0 19.9 + - + +
105C SER* 3.6 4.5 - - - +
107C ARG* 1.3 76.2 - - - +
109C GLY* 1.3 56.9 + - - +
110C SER 3.1 4.6 + - - -
111C LYS 3.4 2.6 + - - -
112C GLY* 2.9 22.0 + - - -
114C VAL* 4.1 13.2 - - + -
166C ALA* 4.0 12.3 - - + +
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Residues in contact with GLY 109 (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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111A LYS* 3.5 7.8 + - - -
105C SER 2.6 21.4 + - - -
106C ILE 3.2 2.8 + - - -
108C ILE* 1.3 69.9 - - - +
110C SER* 1.3 63.2 + - - +
111C LYS 3.0 3.4 + - - -
112C GLY 3.4 21.8 - - - +
114C VAL* 3.7 5.8 - - - -
140C LEU* 3.6 32.5 - - - +
466C PHE* 4.5 0.7 - - - -
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Residues in contact with SER 110 (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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111A LYS* 4.6 0.7 + - - -
142B ASP* 2.9 36.6 + - - +
143B LYS* 4.2 11.3 - - - +
144B HIS* 3.3 24.8 + - - -
106C ILE 3.4 4.0 + - - -
107C ARG 3.5 1.8 - - - -
108C ILE 3.1 1.0 + - - -
109C GLY* 1.3 77.9 - - - +
111C LYS* 1.3 56.4 + - - +
141C ASN* 2.9 29.9 + - - +
466C PHE* 3.8 18.5 - - - -
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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