Contacts of the helix formed by residues 100 - 107 (chain B) in PDB entry 5YL4
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 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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97B ALA 2.8 14.8 + - - +
98B GLY 3.9 5.2 - - - +
99B ASN* 1.3 76.9 - - - +
101B TRP* 1.3 65.5 + - - +
102B ALA* 2.9 34.5 + - - +
103B LYS* 3.2 35.5 + - + +
104B GLY 3.2 9.2 + - - -
142B GLY* 3.6 10.0 - - - -
184B ASN* 4.3 1.1 - - - -
397B TRP* 2.7 42.4 + - - +
398B TYR* 3.4 13.5 - - - -
401B GLU* 4.2 1.6 - - - +
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Residues in contact with TRP 101 (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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100B ASN* 1.3 73.1 + - - +
102B ALA* 1.3 54.3 + - - +
104B GLY* 3.1 2.9 + - - -
105B HIS* 2.7 76.3 + + + +
106B TYR* 3.8 17.5 - + - -
142B GLY* 4.1 6.5 - - - -
145B SER* 3.3 23.8 + - - -
146B GLY* 3.4 18.7 - - - -
149B THR* 3.6 6.7 - - - -
184B ASN* 3.1 32.6 + - - +
187B LEU* 3.6 52.9 - - + -
188B SER* 2.8 19.7 + - - +
191B GLN* 4.0 10.1 - - + -
398B TYR* 3.8 1.3 - - + -
403B MET* 4.3 6.5 - - + -
407B GLU* 3.9 13.5 - - - -
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Residues in contact with ALA 102 (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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100B ASN* 2.9 12.8 + - - +
101B TRP* 1.3 77.8 - - - +
103B LYS* 1.3 59.4 + - - +
106B TYR* 2.8 42.0 + - + +
107B THR* 3.4 3.5 + - - -
398B TYR* 4.2 6.7 - - + +
401B GLU* 3.7 22.9 - - + -
403B MET* 3.6 32.3 - - + -
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Residues in contact with LYS 103 (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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68B LEU* 4.8 0.4 - - - -
95B SER 5.7 2.2 + - - -
96B GLY 4.6 2.3 + - - +
97B ALA* 3.5 31.7 - - - +
98B GLY* 5.2 4.3 - - - +
100B ASN* 3.2 26.3 + - + +
102B ALA* 1.3 78.9 - - - +
104B GLY* 1.3 58.0 + - - +
107B THR* 3.3 10.9 + - - +
108B GLU* 3.0 45.5 + - + +
109B GLY 3.0 8.3 + - - -
401B GLU* 3.5 33.2 - - - +
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Residues in contact with GLY 104 (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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68B LEU* 4.1 15.9 - - - -
97B ALA* 4.4 1.2 - - - +
100B ASN 3.2 4.8 + - - -
101B TRP 3.1 7.1 + - - -
103B LYS* 1.3 79.2 - - - +
105B HIS* 1.3 58.1 + - - +
109B GLY* 3.2 22.3 - - - -
142B GLY 3.6 17.9 - - - -
147B MET* 3.4 21.2 - - - +
150B LEU* 4.1 1.2 - - - +
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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
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101B TRP* 2.7 54.0 + + + +
104B GLY* 1.3 74.9 - - - +
106B TYR* 1.3 84.0 + + + +
110B ALA* 4.7 2.0 + - - +
146B GLY 2.7 22.7 + - - +
149B THR* 3.3 14.9 + - - -
150B LEU* 3.3 58.8 + - + +
153B SER* 5.4 1.9 - - - -
191B GLN* 4.0 15.9 + - - -
75E LYS* 6.3 0.8 - - - +
79E GLU* 4.3 8.0 + - - +
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Residues in contact with TYR 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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101B TRP* 3.8 12.8 - + - -
102B ALA* 2.8 21.5 + - + +
105B HIS* 1.3 99.9 - + + +
107B THR* 1.3 67.3 + - + +
110B ALA* 3.6 15.6 - - - +
401B GLU 4.7 0.7 - - - +
403B MET* 3.7 30.5 - - + -
407B GLU* 2.4 35.6 + - - -
78E HIS* 3.4 14.7 + + - -
79E GLU* 3.9 33.4 - - + +
82E VAL* 3.6 35.9 - - + -
83E ILE* 3.7 17.7 - - - +
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Residues in contact with THR 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 ALA 3.4 1.6 + - - -
103B LYS* 3.3 15.5 + - - +
106B TYR* 1.3 82.7 - - + +
108B GLU* 1.3 78.8 + - - +
109B GLY 3.3 1.2 + - - +
110B ALA* 3.4 10.9 + - - +
111B GLU* 3.4 12.5 + - - +
401B GLU* 2.8 53.8 + - + +
83E ILE* 4.3 23.4 - - + +
86E ALA* 4.6 7.6 - - + -
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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