Contacts of the helix formed by residues 105 - 111 (chain B) in PDB entry 1IVH
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 ILE 105 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61B LEU 3.4 24.7 - - - +
62B GLY* 4.4 1.6 - - - -
64B THR* 5.6 2.0 - - - +
65B ALA* 4.4 13.5 - - + +
100B HIS* 3.0 39.2 + - + +
101B SER 3.4 13.2 - - - +
102B ASN 3.9 0.2 + - - -
104B CYS* 1.3 76.3 - - - +
106B ASN* 1.3 66.5 + - - +
108B LEU* 2.9 19.3 + - - +
109B VAL* 3.0 23.7 + - + +
121B LEU* 3.9 14.8 - - + -
124B LEU* 3.6 36.3 - - + +
125B ILE* 4.1 4.5 - - + +
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Residues in contact with ASN 106 (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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64B THR* 3.8 17.5 + - - +
76B TYR* 2.9 40.6 + - - -
79B HIS* 5.8 0.2 - - + -
101B SER 3.3 7.7 + - - +
102B ASN* 3.1 32.2 + - - +
105B ILE* 1.3 81.8 - - - +
107B GLN* 1.3 59.0 + - - +
109B VAL* 3.2 22.5 - - - +
110B ARG* 3.1 29.5 + - - +
253B LEU* 3.8 15.2 - - - +
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Residues in contact with GLN 107 (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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102B ASN 3.5 3.2 + - - +
103B LEU* 3.3 23.3 - - - +
104B CYS 3.3 3.7 + - - +
105B ILE 3.2 0.4 - - - -
106B ASN* 1.3 80.3 + - - +
108B LEU* 1.3 58.1 + - - +
110B ARG* 4.4 11.1 - - - -
111B ASN* 3.1 40.7 + - - +
133B LEU* 4.7 3.9 - - + +
177B ILE* 3.7 13.9 - - + -
179B TYR* 3.1 20.3 + - - +
237B LEU* 4.1 9.3 - - + +
246B VAL* 2.7 31.2 + - + +
247B LEU* 4.4 0.8 + - - +
249B SER* 5.6 0.2 - - - -
250B GLY* 3.4 23.2 + - - -
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Residues in contact with LEU 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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104B CYS* 3.1 34.3 + - - +
105B ILE* 2.9 12.2 + - - +
107B GLN* 1.3 76.5 - - - +
109B VAL* 1.3 59.2 + - - +
110B ARG 3.2 0.4 - - - -
112B GLY* 3.1 27.0 + - - +
116B GLN* 4.8 17.3 - - + +
117B LYS* 3.4 11.5 - - + +
120B TYR* 4.5 14.4 - - + -
121B LEU* 4.3 13.2 - - + -
124B LEU* 4.8 7.2 - - + -
175B VAL* 4.4 14.4 - - + -
177B ILE* 4.1 8.5 - - + -
197B ILE* 3.8 30.3 - - + -
237B LEU* 4.6 10.1 - - + -
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Residues in contact with VAL 109 (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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64B THR 4.5 10.1 - - - +
65B ALA* 4.0 19.1 - - + -
66B PRO* 4.0 15.1 - - + +
105B ILE* 3.0 19.4 + - + +
106B ASN* 3.2 26.2 - - - +
108B LEU* 1.3 76.2 - - - +
110B ARG* 1.3 69.0 + - + +
112B GLY 4.9 1.2 - - - +
117B LYS* 3.9 23.1 + - - +
121B LEU* 3.6 23.6 - - + -
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Residues in contact with ARG 110 (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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76B TYR* 3.9 6.4 + - - +
106B ASN* 3.1 27.6 + - - +
107B GLN* 3.9 14.1 - - - +
108B LEU 3.2 0.2 - - - -
109B VAL* 1.3 86.4 - - + +
111B ASN* 1.3 76.7 + - - +
112B GLY 4.8 1.9 - - - +
249B SER* 4.8 18.8 + - - -
250B GLY* 5.9 0.4 - - - -
253B LEU* 3.0 37.7 - - - +
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Residues in contact with ASN 111 (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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107B GLN* 3.1 22.3 + - - +
110B ARG* 1.3 93.6 + - - +
112B GLY* 1.3 66.1 + - - +
113B ASN 3.8 0.3 + - - -
116B GLN* 4.3 0.3 - - - +
237B LEU* 3.4 18.1 - - + +
238B GLY* 3.5 25.2 + - - +
246B VAL* 3.3 42.7 - - + +
249B SER* 5.0 4.0 + - - -
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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