Contacts of the helix formed by residues 123 - 132 (chain A) in PDB entry 1Y8B
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 123 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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120A PRO* 3.2 25.8 + - + +
122A MET* 1.3 93.3 - - - +
124A ALA* 1.3 63.8 + - - +
125A ARG* 3.2 18.5 - - - +
126A TYR* 3.4 23.8 - - + +
127A ALA* 3.6 15.4 + - - +
289A ASN* 4.5 1.1 - - - -
293A LEU* 5.8 0.7 - - - +
606A TYR* 6.1 0.2 - - - -
610A TRP* 3.5 26.6 - - - -
615A ILE* 3.9 1.4 - - - +
616A GLY* 3.8 25.5 - - - +
631A ASP* 6.3 1.3 - - - +
632A ARG* 4.6 2.6 - - - +
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Residues in contact with ALA 124 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET 3.6 3.2 + - - -
123A ASN* 1.3 68.4 - - - +
125A ARG* 1.3 83.4 + - + +
126A TYR 3.2 0.7 - - - -
127A ALA* 2.7 18.2 + - - +
128A LEU* 2.8 11.2 + - - +
289A ASN* 3.7 26.9 + - + +
293A LEU* 6.2 1.8 - - - -
298A LEU* 4.8 8.2 - - + +
299A GLN* 4.2 24.7 - - + +
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Residues in contact with ARG 125 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A MET 4.4 1.8 + - - -
123A ASN* 3.2 29.8 - - - +
124A ALA* 1.3 95.8 - - + +
126A TYR* 1.3 64.8 + - - +
128A LEU* 2.8 5.8 + - - -
129A ASN* 2.7 28.7 + - + +
289A ASN* 5.3 0.6 + - - -
299A GLN* 3.9 9.4 + - + +
300A GLU* 3.7 11.7 - - + -
301A LYS* 3.7 52.9 - - + +
614A GLY 4.1 4.8 + - - -
615A ILE* 3.7 30.9 - - - +
616A GLY 5.2 0.4 - - - -
617A CYS* 3.9 25.8 - - + -
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Residues in contact with TYR 126 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 4.3 8.5 - - + -
118A VAL 4.2 10.4 + - - -
119A VAL* 4.4 3.1 - - - -
120A PRO* 3.6 29.6 - - + -
123A ASN* 3.4 25.6 - - + +
124A ALA 3.2 0.6 - - - +
125A ARG* 1.3 80.4 - - - +
127A ALA* 1.3 57.9 + - - +
129A ASN* 4.2 5.4 - - - +
130A ALA* 3.1 25.6 + - + +
536A PRO* 2.4 34.3 + - - +
616A GLY 3.3 24.7 - - - +
617A CYS* 4.4 9.2 - - + +
629A MET* 3.6 22.9 - - + +
631A ASP* 3.7 31.6 + - + -
636A ARG* 5.4 0.4 + - - -
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Residues in contact with ALA 127 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 4.0 31.8 - - + +
123A ASN 3.6 12.3 + - - +
124A ALA* 2.7 17.3 + - - +
126A TYR* 1.3 73.2 - - - +
128A LEU* 1.3 52.1 + - - +
131A ALA* 2.4 45.5 + - + +
269A LEU* 5.5 0.4 - - + -
293A LEU* 4.3 19.3 - - + -
298A LEU* 4.4 5.2 - - + -
335A LEU* 6.4 0.9 - - + -
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Residues in contact with LEU 128 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124A ALA 2.8 9.3 + - - +
125A ARG* 2.8 15.5 + - - +
127A ALA* 1.3 73.0 - - - +
129A ASN* 1.3 59.0 + - - +
131A ALA* 4.1 3.8 - - - -
132A ASN* 2.7 74.3 + - + +
298A LEU* 3.4 19.9 - - + +
299A GLN* 3.0 48.2 - - - +
300A GLU* 3.7 23.1 - - + +
312A LYS 4.1 11.0 - - - +
313A LEU* 5.6 0.7 - - - -
332A ARG* 4.5 2.2 - - - +
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Residues in contact with ASN 129 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A ARG* 2.7 21.1 + - + +
126A TYR* 4.2 4.7 - - - +
128A LEU* 1.3 74.2 - - - +
130A ALA* 1.3 61.0 + - - +
132A ASN* 4.3 2.6 - - - +
133A ALA* 3.4 16.6 + - - +
300A GLU* 4.8 9.3 + - + +
538A PRO* 4.6 10.2 - - - +
617A CYS* 6.2 2.2 - - + -
618A SER* 5.8 5.8 - - - +
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Residues in contact with ALA 130 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117A LEU* 3.6 37.4 - - + +
119A VAL* 4.3 5.8 - - + -
126A TYR* 3.1 25.8 + - + +
127A ALA 3.9 0.7 - - - +
129A ASN* 1.3 80.9 - - - +
131A ALA* 1.3 63.2 + - - +
133A ALA* 2.9 24.4 - - - +
134A ARG 4.3 0.2 + - - -
264A ALA* 4.5 11.1 - - - +
267A THR* 5.7 0.7 - - - -
538A PRO* 4.1 6.9 - - + +
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Residues in contact with ALA 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A VAL* 5.3 3.3 - - + +
127A ALA* 2.4 38.7 + - + +
128A LEU 3.9 0.9 - - - +
130A ALA* 1.3 66.5 - - - +
132A ASN* 1.3 55.9 + - - +
133A ALA 2.6 15.0 + - - -
134A ARG* 3.1 10.0 + - - +
267A THR* 5.4 2.7 - - - -
298A LEU* 5.2 0.4 - - + -
332A ARG* 3.9 23.6 - - - +
333A SER* 3.2 35.3 + - - -
335A LEU* 4.4 13.7 - - + -
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Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A LEU* 2.7 47.0 + - + +
129A ASN* 4.3 3.1 - - - +
131A ALA* 1.3 68.4 - - - +
133A ALA* 1.3 57.9 + - - +
134A ARG 3.1 4.5 + - - -
135A TRP 3.6 17.9 + - - +
136A GLY* 5.2 0.3 - - - -
300A GLU* 4.8 2.4 + - - -
312A LYS* 3.6 9.7 + - - +
313A LEU 3.7 1.0 + - - -
314A ASN* 3.4 52.9 + - - +
332A ARG* 3.8 13.5 + - - -
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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