Contacts of the helix formed by residues 99 - 108 (chain H) in PDB entry 3IYD
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 TYR 99 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36H ALA* 3.4 31.5 - - + +
37H GLU* 3.5 4.3 + - - +
38H THR 3.1 42.7 + - - -
39H LEU* 4.0 19.3 - - + -
71H GLY 2.8 25.5 + - - -
72H GLU* 5.1 0.2 - - - -
74H GLY* 3.6 21.8 - - - -
75H LEU* 3.4 30.3 - - + -
82H ARG* 3.5 12.0 + - - -
98H SER* 1.3 70.9 - - - +
100H LYS* 1.3 65.1 + - - +
102H PHE* 3.4 5.4 - - - +
103H ARG* 3.0 50.4 + - - +
680H CMP 4.8 0.3 + - - -
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Residues in contact with LYS 100 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ASN* 6.1 0.6 - - - +
98H SER* 3.2 7.9 - - - +
99H TYR* 1.3 80.6 - - - +
101H LYS* 1.3 72.5 + - + +
102H PHE 3.4 0.2 + - - -
103H ARG* 3.4 21.1 + - - +
104H GLN* 3.7 29.3 + - - +
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Residues in contact with LYS 101 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H ILE* 5.2 5.4 - - + -
98H SER* 3.4 25.3 + - - +
99H TYR 3.3 0.2 - - - -
100H LYS* 1.3 87.2 - - + +
102H PHE* 1.3 58.3 + - - +
103H ARG 3.5 0.2 - - - -
104H GLN* 3.8 18.0 + - - +
105H LEU* 3.3 27.9 + - + +
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Residues in contact with PHE 102 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14H PHE* 3.4 33.7 - + - -
39H LEU* 4.0 17.5 - - + -
69H PHE* 6.4 0.4 - + - -
75H LEU* 3.4 35.7 - - + -
97H ILE* 4.2 11.0 - - + -
98H SER 3.2 16.3 + - - +
99H TYR* 3.1 11.1 + - - +
101H LYS* 1.3 76.6 - - - +
103H ARG* 1.3 65.5 + - - +
104H GLN 3.1 1.6 - - - -
105H LEU* 3.0 24.4 + - + +
106H ILE* 3.4 32.8 + - + +
112H ILE* 3.5 28.9 - - + -
113H LEU* 4.9 4.0 - - + -
116H LEU* 4.7 8.7 - - + -
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Residues in contact with ARG 103 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114G MET* 5.5 8.2 - - + +
74H GLY 4.5 6.5 + - - -
75H LEU* 3.7 28.6 + - + +
76H PHE 5.4 1.2 + - - -
78H GLU* 3.5 43.9 - - - +
99H TYR* 3.0 51.9 + - - +
100H LYS* 3.4 14.4 - - - +
101H LYS 3.5 0.2 - - - -
102H PHE* 1.3 75.9 - - - +
104H GLN* 1.3 62.2 + - + +
106H ILE* 3.4 21.8 + - + +
107H GLN* 3.5 25.9 + - - +
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Residues in contact with GLN 104 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100H LYS* 3.7 31.3 + - - +
101H LYS* 4.0 15.4 - - - +
102H PHE 3.1 0.6 - - - -
103H ARG* 1.3 77.4 - - + +
105H LEU* 1.3 62.4 + - + +
106H ILE 3.3 0.2 - - - -
107H GLN* 3.9 10.9 + - - +
108H VAL* 3.3 27.7 + - - +
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Residues in contact with LEU 105 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TRP* 3.6 39.2 - - + +
14H PHE* 5.7 4.9 - - + -
17H HIS* 5.1 23.6 - - + +
97H ILE* 5.5 7.9 - - + -
101H LYS* 3.3 19.7 - - + +
102H PHE* 3.0 24.1 + - + +
104H GLN* 1.3 80.0 - - + +
106H ILE* 1.3 60.4 + - - +
107H GLN 3.5 0.2 - - - -
108H VAL* 3.4 10.0 - - + +
109H ASN* 3.0 30.4 + - - +
112H ILE* 4.1 7.1 - - + +
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Residues in contact with ILE 106 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G PRO* 5.2 7.8 - - + +
114G MET* 5.0 15.5 - - + -
75H LEU* 4.9 5.2 - - + -
102H PHE* 3.4 43.3 - - + +
103H ARG* 3.7 13.5 - - + +
104H GLN 3.3 0.6 - - - -
105H LEU* 1.3 77.1 - - - +
107H GLN* 1.3 65.3 + - + +
108H VAL 3.1 1.8 - - - -
109H ASN 3.8 4.7 - - - -
110H PRO* 3.0 33.7 - - + +
112H ILE* 4.2 8.3 - - + -
113H LEU* 3.8 42.2 - - + -
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Residues in contact with GLN 107 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110G PRO* 5.5 10.9 - - - +
103H ARG* 3.5 22.5 + - - +
104H GLN* 4.3 10.7 - - - +
105H LEU 3.5 0.4 - - - -
106H ILE* 1.3 77.1 - - + +
108H VAL* 1.3 63.2 + - + +
110H PRO* 4.8 3.3 - - - +
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Residues in contact with VAL 108 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13H TRP* 5.1 5.4 - - + -
104H GLN 3.3 21.1 - - - +
105H LEU* 3.4 18.8 - - + +
107H GLN* 1.3 81.3 - - + +
109H ASN* 1.3 67.8 + - + +
110H PRO* 4.0 3.7 - - - +
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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