Contacts of the helix formed by residues 90 - 102 (chain A) in PDB entry 1YA8
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 ASP 90 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A GLN* 1.3 73.6 - - - +
91A PRO* 1.3 67.0 - - - +
92A LYS* 2.8 25.7 + - - +
93A ALA* 3.5 26.7 + - + +
94A GLY* 2.8 29.6 + - - -
145A MET 5.0 0.4 + - - -
146A VAL* 4.5 4.4 - - + +
295A LEU* 4.6 1.7 - - - +
298A THR* 5.5 6.4 - - + +
299A LEU* 3.8 26.4 - - + +
304A LEU* 4.3 13.9 - - + +
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Residues in contact with PRO 91 (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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86A MET* 5.1 6.6 - - + +
89A GLN 2.8 11.0 - - - +
90A ASP* 1.3 88.3 - - - +
92A LYS* 1.3 75.3 + - + +
94A GLY* 4.0 1.2 - - - +
95A GLN* 3.2 22.0 + - - +
112A LEU* 3.9 26.7 - - + -
295A LEU* 4.4 12.8 - - + -
299A LEU* 5.0 7.4 - - + -
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Residues in contact with LYS 92 (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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90A ASP* 2.8 19.2 + - - +
91A PRO* 1.3 83.8 - - + +
93A ALA* 1.3 62.8 + - - +
94A GLY 3.2 0.2 + - - -
95A GLN* 3.3 4.3 + - - +
96A LEU* 3.2 18.5 + - - +
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Residues in contact with ALA 93 (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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90A ASP* 3.2 17.2 + - + +
92A LYS* 1.3 79.6 - - - +
94A GLY* 1.3 63.6 + - - +
96A LEU* 3.3 8.8 + - - +
97A LEU* 3.0 24.6 + - - +
146A VAL* 4.4 9.4 - - + +
304A LEU* 3.7 30.1 - - + -
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Residues in contact with GLY 94 (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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86A MET* 5.0 9.0 - - - +
89A GLN* 3.4 26.7 - - - -
90A ASP 2.8 17.8 + - - -
91A PRO 4.0 1.1 - - - -
92A LYS 3.2 0.2 - - - -
93A ALA* 1.3 72.9 - - - +
95A GLN* 1.3 65.1 + - - +
97A LEU* 3.3 2.6 + - - +
98A SER* 3.1 22.9 + - - -
146A VAL* 4.4 5.8 - - - +
147A GLY* 5.2 2.1 + - - -
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Residues in contact with GLN 95 (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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86A MET* 5.0 5.8 - - + +
91A PRO 3.2 17.8 + - - +
92A LYS* 3.3 4.0 + - - +
94A GLY* 1.3 74.6 - - - +
96A LEU* 1.3 60.8 + - - +
98A SER* 3.3 6.6 + - - -
99A GLU* 2.9 55.2 + - + +
107A ASN* 4.7 6.7 - - - +
109A PRO* 4.4 19.3 - - + +
110A LEU 5.6 0.3 + - - -
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Residues in contact with LEU 96 (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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92A LYS 3.2 10.8 + - - +
93A ALA* 3.6 11.7 - - - +
94A GLY 3.1 0.8 - - - -
95A GLN* 1.3 80.5 - - - +
97A LEU* 1.3 61.9 + - - +
99A GLU* 3.4 18.2 + - + +
100A LEU* 3.2 40.1 + - + +
361A MET* 5.1 6.3 - - + -
363A LEU* 3.7 25.4 - - + -
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Residues in contact with LEU 97 (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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93A ALA 3.0 15.6 + - - +
94A GLY 4.0 3.1 - - - +
96A LEU* 1.3 73.5 - - - +
98A SER* 1.3 65.1 + - - +
100A LEU* 3.4 9.0 + - + +
101A PHE* 3.0 61.7 + - + +
141A GLY 4.3 6.5 - - - +
142A GLY* 3.8 17.5 - - - -
146A VAL* 3.8 30.3 - - + +
147A GLY* 5.0 4.3 - - - +
152A TYR* 5.6 0.9 - - - +
358A LEU* 5.0 0.7 - - + -
363A LEU* 4.4 17.9 - - + +
4001A SMB 4.1 17.5 - - + +
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Residues in contact with SER 98 (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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86A MET* 6.6 0.2 - - - -
94A GLY 3.1 17.7 + - - -
95A GLN* 3.5 7.2 - - - -
97A LEU* 1.3 78.0 - - - +
99A GLU* 1.3 56.3 + - - +
102A THR* 2.8 32.7 + - - -
107A ASN* 2.6 32.3 + - - -
108A ILE 4.5 5.2 + - - -
110A LEU* 5.4 5.6 - - - +
148A ALA* 6.3 0.2 - - - -
151A THR* 2.8 33.3 + - - +
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Residues in contact with GLU 99 (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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95A GLN* 2.9 41.0 + - + +
96A LEU* 3.8 22.2 - - + +
97A LEU 3.3 0.2 - - - -
98A SER* 1.3 76.2 - - - +
100A LEU* 1.3 62.6 + - + +
102A THR* 3.3 14.5 - - - +
107A ASN* 3.4 29.4 - - + +
482A LYS* 4.7 6.1 + - - -
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Residues in contact with LEU 100 (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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96A LEU* 3.2 42.4 + - + +
97A LEU* 3.8 7.6 - - + +
98A SER 3.2 0.2 - - - -
99A GLU* 1.3 79.7 - - + +
101A PHE* 1.3 68.5 + - + +
357A TRP* 4.7 7.6 - - + -
358A LEU* 3.6 31.2 - - + -
361A MET* 4.1 11.4 - - + -
363A LEU* 4.2 5.4 - - + -
455A PHE 5.6 0.2 - - - +
457A SER* 4.1 26.9 - - - +
473A PHE* 3.4 22.4 - - - -
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Residues in contact with PHE 101 (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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97A LEU* 3.0 44.8 + - + +
100A LEU* 1.3 88.6 - - + +
102A THR* 1.3 67.9 + - - +
103A ASN* 3.4 4.0 + - - +
141A GLY 5.6 3.6 - - - -
151A THR* 4.2 6.1 - - + -
152A TYR* 3.2 38.1 - - + +
220A GLU* 3.7 22.2 - - - -
221A SER* 5.6 0.2 - - - -
358A LEU* 3.3 35.9 - - + -
468A HIS* 4.3 8.3 - + - -
469A GLY* 3.9 20.2 - - - -
472A LEU* 4.0 20.8 - - + +
473A PHE* 4.4 8.7 - + - -
4001A SMB 4.5 5.6 - - - -
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Residues in contact with THR 102 (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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98A SER* 2.8 25.0 + - - +
99A GLU* 3.3 16.3 - - - +
101A PHE* 1.3 74.1 - - - +
103A ASN* 1.3 60.1 + - - +
104A ARG* 3.1 36.6 + - - +
107A ASN* 3.5 24.9 + - + +
151A THR* 3.3 23.0 + - - +
152A TYR* 5.7 0.2 - - - -
473A PHE* 3.8 5.5 - - - -
482A LYS* 3.3 20.2 + - - +
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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