Contacts of the helix formed by residues 101 - 112 (chain B) in PDB entry 1YRT
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 SER 101 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99B TYR* 3.9 1.6 + - - +
100B ILE* 1.3 74.5 - - - +
102B ALA* 1.3 60.3 + - - +
103B ALA* 3.6 8.4 + - - +
104B GLU* 3.1 34.5 + - - +
105B LEU* 3.0 28.6 + - - +
125B ILE* 3.6 4.2 - - - +
134B GLY 5.2 0.9 - - - -
135B GLN* 4.5 12.3 - - - +
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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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101B SER* 1.3 75.3 - - - +
103B ALA* 1.4 55.5 + - - +
105B LEU 3.5 0.3 + - - -
106B ARG* 2.9 26.9 + - - +
121B VAL* 3.3 21.2 - - + +
122B ASP* 5.3 5.6 - - + +
125B ILE* 3.1 25.0 - - + +
134B GLY 5.0 5.7 + - - +
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Residues in contact with ALA 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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101B SER* 3.2 9.2 + - - +
102B ALA* 1.4 73.6 - - - +
104B GLU* 1.3 68.5 + - + +
106B ARG* 3.3 18.1 + - - +
107B HIS* 3.1 35.3 + - + +
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Residues in contact with GLU 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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92B PHE 3.4 16.0 - - - +
93B ASP* 3.8 0.5 - - - +
94B LYS* 3.6 23.7 + - + +
95B ASP* 3.0 31.4 + - + +
99B TYR 3.1 3.8 - - - +
100B ILE* 3.4 4.2 - - + -
101B SER* 3.1 33.5 + - - +
103B ALA* 1.3 78.8 - - + +
105B LEU* 1.3 62.1 + - - +
107B HIS* 3.0 13.0 + - - +
108B VAL* 3.0 25.3 + - - +
801B CA 2.5 30.9 - - - -
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Residues in contact with LEU 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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242A TRP* 4.0 22.4 - - + -
92B PHE* 4.0 26.2 - - + -
100B ILE* 4.4 10.4 - - + +
101B SER 3.0 18.0 + - - +
102B ALA 3.6 4.5 - - - +
104B GLU* 1.3 76.1 - - - +
106B ARG* 1.3 64.5 + - - +
108B VAL* 3.2 5.5 + - + -
109B MET* 2.9 45.7 + - + +
121B VAL* 4.3 3.8 - - + +
124B MET* 3.4 40.6 - - + -
125B ILE* 3.9 19.7 - - + -
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Residues in contact with ARG 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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102B ALA 2.9 18.5 + - - +
103B ALA* 3.6 15.7 + - - +
105B LEU* 1.3 77.7 - - - +
107B HIS* 1.3 73.7 + - - +
109B MET* 3.4 5.7 + - - +
110B THR* 3.0 35.0 + - - +
116B LEU* 4.5 16.1 + - + +
118B ASP* 4.0 22.5 + - - -
121B VAL* 3.8 24.4 - - + +
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Residues in contact with HIS 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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94B LYS* 3.9 37.3 + - + -
103B ALA* 3.1 32.0 + - + +
104B GLU* 3.0 8.6 + - + +
106B ARG* 1.3 91.1 + - + +
108B VAL* 1.3 65.1 + - - +
110B THR* 3.6 7.9 + - - +
111B ASN* 3.1 34.0 + - - +
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Residues in contact with VAL 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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198A LEU* 3.9 23.1 - - + -
245A ALA* 4.4 0.9 - - + -
249A ALA* 6.4 0.2 - - + -
91B VAL* 4.3 4.0 - - + +
92B PHE* 3.9 56.3 - - + +
94B LYS* 5.6 3.8 - - + -
104B GLU 3.0 16.6 + - - +
105B LEU* 3.2 8.9 + - - +
107B HIS* 1.3 77.2 - - + +
109B MET* 1.3 67.5 + - - +
111B ASN* 3.3 2.6 + - - +
112B LEU* 2.9 49.2 + - + +
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Residues in contact with MET 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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241A LEU* 3.8 17.9 - - + +
244A ILE* 3.5 34.5 - - + -
245A ALA* 3.6 29.4 - - - -
105B LEU* 2.9 24.8 + - + +
106B ARG* 3.4 5.8 + - - +
107B HIS 3.3 0.2 - - - -
108B VAL* 1.3 76.2 - - - +
110B THR* 1.3 63.6 + - - +
112B LEU* 3.3 3.0 + - - +
113B GLY 3.3 4.5 + - - -
114B GLU* 2.7 49.6 + - + +
116B LEU* 3.7 9.2 - - + -
124B MET* 3.5 29.2 - - + +
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Residues in contact with THR 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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106B ARG* 3.0 23.7 + - - +
107B HIS* 3.8 9.6 - - - +
109B MET* 1.3 76.0 - - - +
111B ASN* 1.3 76.8 + - - +
113B GLY* 2.8 12.5 + - - -
114B GLU 3.4 17.1 + - - +
115B LYS* 4.3 17.2 - - + +
116B LEU 4.9 0.7 + - - -
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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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197A HIS* 3.2 33.4 + - - -
198A LEU* 3.9 19.7 - - + +
199A SER* 3.3 38.3 - - - +
202A ARG* 3.9 8.7 - - - +
341A GLY* 4.5 7.4 - - - -
94B LYS* 6.1 0.2 - - - +
107B HIS* 3.1 24.0 + - - +
108B VAL 3.7 4.3 - - - +
109B MET 3.2 0.4 - - - -
110B THR* 1.3 87.6 - - - +
112B LEU* 1.3 61.2 + - - +
113B GLY 3.1 4.0 + - - -
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Residues in contact with LEU 112 (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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198A LEU* 3.9 23.8 - - + +
201A PHE* 3.8 31.0 - - + +
202A ARG* 3.7 16.7 - - - +
205A ALA* 4.6 1.1 - - + -
206A ARG* 4.8 2.8 + - - +
244A ILE* 3.4 33.3 - - + +
245A ALA* 3.8 30.7 - - - +
248A GLY* 3.9 19.3 - - - -
249A ALA 4.8 0.2 - - - +
108B VAL* 2.9 32.8 + - + +
109B MET* 3.4 6.1 - - - +
110B THR 3.0 0.2 - - - -
111B ASN* 1.3 77.0 - - - +
113B GLY* 1.3 59.3 + - - -
114B GLU* 3.5 2.8 + - - +
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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