Contacts of the helix formed by residues 104 - 108 (chain B) in PDB entry 3MH5
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B THR 3.7 1.0 + - - -
103B ASN* 1.3 66.5 - - - +
105B HIS* 1.3 59.3 + - - +
106B VAL 2.9 11.7 + - - -
107B VAL* 5.0 0.8 - - - +
108B ASP* 3.0 42.5 + - - +
130B LYS* 2.9 50.5 - - - +
131B ASP 3.6 5.4 - - - +
132B PRO* 4.0 19.2 - - + +
135B ASP* 2.8 31.1 + - - +
136B ILE 4.0 7.0 - - - +
137B ALA* 3.8 8.9 - - - +
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Residues in contact with HIS 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B ALA* 5.1 4.2 - - - +
103B ASN* 3.4 21.8 + - + +
104B ASN* 1.3 78.3 + - - +
106B VAL* 1.3 71.2 + - + +
108B ASP* 4.5 7.1 - - - +
135B ASP* 2.7 39.8 + - - +
207B ARG 5.3 0.7 - - - -
208B GLY* 3.2 33.5 + - - -
210B SER 5.8 0.2 - - - -
211B GLY* 5.1 4.2 - - - -
227B ALA* 4.8 13.2 + - + +
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Residues in contact with VAL 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.8 6.3 - - + -
31B VAL* 3.1 35.2 - - + +
84B PHE* 5.0 0.9 - - - -
86B ALA* 3.7 11.0 - - + +
87B LEU 3.6 13.0 - - - +
88B GLY* 3.6 35.9 - - - +
89B SER 5.6 0.7 - - - +
102B THR* 4.8 4.7 - - - +
103B ASN* 3.6 24.0 - - + +
104B ASN 2.9 1.0 - - - -
105B HIS* 1.3 106.0 - - + +
107B VAL* 1.3 64.3 + - + +
108B ASP 3.4 4.4 + - - +
208B GLY 5.4 1.1 - - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B ILE* 4.5 9.6 - - + -
31B VAL* 4.3 12.6 - - + -
102B THR* 4.0 13.2 - - + -
103B ASN 3.6 6.3 - - - +
104B ASN* 3.9 5.6 - - - +
106B VAL* 1.3 79.5 - - + +
108B ASP* 1.3 66.7 + - - +
109B ASN 3.4 0.2 + - - -
110B ALA* 3.2 20.6 + - - +
113B ILE* 3.9 11.7 - - + -
127B MET* 3.8 27.2 - - - +
130B LYS* 5.1 0.4 + - + -
137B ALA* 3.4 32.8 - - + -
139B ILE* 3.9 20.4 - - + -
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Residues in contact with ASP 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84B PHE* 3.4 14.4 - - - -
104B ASN* 3.0 32.2 + - - +
105B HIS* 4.7 7.1 - - - -
106B VAL 3.4 2.6 - - - +
107B VAL* 1.3 75.5 - - - +
109B ASN* 1.3 107.0 + - - +
110B ALA* 4.3 0.2 - - - -
130B LYS* 2.9 29.5 + - - +
132B PRO* 4.9 4.7 - - - +
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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