Contacts of the helix formed by residues 91 - 102 (chain A) in PDB entry 1YSD
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 CYS 91 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62A HIS* 3.5 8.7 - - + -
89A SER 3.8 1.8 + - - -
90A PRO* 1.3 78.4 - - - +
92A ASP* 1.3 58.2 + - - +
93A MET* 3.3 23.3 - - - -
94A CYS 3.5 3.6 - - - -
95A THR* 2.9 25.5 + - - -
114A PHE* 3.8 23.0 - - + -
116A SER* 3.4 8.7 - - - -
156A ILE* 5.2 1.6 - - + -
500A ZN 4.1 2.8 - - - -
501A ZN 2.4 38.3 - - - -
300B MET* 3.6 19.5 - - + -
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Residues in contact with ASP 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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91A CYS* 1.3 76.5 - - - +
93A MET* 1.3 56.3 + - - +
95A THR* 3.7 6.8 - - - +
96A GLY* 3.0 20.6 + - - -
116A SER* 3.6 13.6 + - - -
117A LYS 4.7 0.2 + - - -
118A GLY* 3.7 17.7 + - - -
121A TYR* 6.1 0.3 - - - -
296B GLY* 3.3 25.4 - - - +
299B ILE* 3.5 23.3 - - + +
300B MET* 4.1 9.5 - - + +
321B TYR* 4.3 3.2 + - + -
325B ARG* 2.9 32.6 + - - -
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Residues in contact with MET 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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59A ALA 5.3 0.4 - - - +
60A THR* 3.5 38.4 - - - +
62A HIS* 3.6 32.1 - - + +
65A ILE* 3.9 16.8 - - + -
91A CYS* 3.2 8.4 - - - -
92A ASP* 1.3 77.0 - - - +
94A CYS* 1.3 65.3 + - - +
96A GLY* 3.0 3.5 + - - -
97A ALA* 3.0 20.8 + - - +
501A ZN 4.3 0.9 - - - -
265B ILE* 4.6 11.4 - - + -
268B LEU* 5.7 0.2 - - - -
293B MET* 4.1 8.2 - - + +
296B GLY* 3.4 11.4 + - - +
297B ALA* 3.7 36.3 - - + +
300B MET* 4.1 13.9 - - + +
301B TYR* 5.3 2.2 - - - -
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Residues in contact with CYS 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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62A HIS* 3.6 18.6 - - - -
64A GLU* 3.6 40.4 - - + +
65A ILE* 3.8 19.1 - - - -
90A PRO* 3.9 10.3 - - + -
91A CYS* 3.4 2.2 + - - +
93A MET* 1.3 80.6 - - - +
95A THR* 1.3 61.8 + - - +
97A ALA* 3.2 3.5 + - - +
98A ILE* 3.1 26.9 + - - +
501A ZN 2.3 34.5 - - - -
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Residues in contact with THR 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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90A PRO* 3.5 16.8 + - - +
91A CYS 2.9 22.5 + - - -
92A ASP* 3.7 5.4 - - - +
94A CYS* 1.3 77.3 - - - +
96A GLY* 1.3 63.0 + - - +
98A ILE* 3.2 5.6 + - - +
99A ILE* 3.0 36.1 + - + +
118A GLY* 3.3 42.9 + - - +
121A TYR* 4.2 9.2 - - + -
122A LEU* 3.5 19.0 - - + +
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Residues in contact with GLY 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 ASP 3.0 10.5 + - - -
93A MET 3.0 8.4 + - - -
95A THR* 1.3 79.8 - - - +
97A ALA* 1.3 55.0 + - - +
99A ILE* 3.4 8.9 + - - +
100A MET* 2.8 30.8 + - - +
121A TYR* 6.2 0.9 - - - -
292B ASP* 3.3 22.8 - - - -
293B MET* 3.4 10.0 + - - -
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Residues in contact with ALA 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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64A GLU* 6.3 0.2 - - + -
65A ILE* 3.9 11.9 - - + -
68A LEU* 3.8 23.1 - - + +
93A MET 3.0 9.9 + - - +
94A CYS 3.5 9.2 - - - +
95A THR 3.2 0.4 - - - -
96A GLY* 1.3 74.8 - - - +
98A ILE* 1.3 65.2 + - - +
100A MET* 3.8 1.4 - - - +
101A TYR* 3.1 30.9 + - + +
293B MET* 3.8 29.8 - - - +
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Residues in contact with ILE 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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64A GLU* 5.6 0.4 - - + -
68A LEU* 5.8 0.2 - - + -
84A LEU* 3.5 33.9 - - + -
90A PRO* 4.6 6.5 - - + -
94A CYS* 3.1 16.0 + - + +
95A THR* 3.5 8.7 - - - +
97A ALA* 1.3 77.0 - - + +
99A ILE* 1.3 62.9 + - - +
101A TYR 3.7 0.3 + - - -
102A GLY 3.1 17.2 + - - -
103A ILE* 3.1 47.3 + - + +
106A CYS* 3.7 32.5 - - + -
122A LEU* 3.7 26.0 - - + -
127A HIS* 3.6 5.1 - - + +
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Residues in contact with ILE 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 THR* 3.0 25.8 + - + +
96A GLY* 3.6 6.1 - - - +
98A ILE* 1.3 74.5 - - - +
100A MET* 1.3 67.0 + - - +
102A GLY* 3.1 12.6 + - - -
121A TYR* 3.5 39.3 - - + +
122A LEU* 3.7 13.9 - - + -
125A ARG* 3.4 42.8 - - + +
127A HIS* 3.6 20.4 + - + +
292B ASP* 3.5 14.5 - - + +
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Residues in contact with MET 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 GLY 2.8 22.0 + - - +
97A ALA 3.4 2.4 + - - +
99A ILE* 1.3 78.3 - - - +
101A TYR* 1.3 96.7 + - + +
102A GLY 3.5 0.2 + - - -
262B HIS* 3.7 25.4 - - + +
291B CYS* 3.7 25.6 - - + -
292B ASP* 4.4 8.1 - - + +
293B MET* 4.1 21.3 - - + +
355B ASP 4.0 1.1 - - - +
356B ILE* 3.7 38.4 - - + +
357B GLY* 4.0 3.6 - - - +
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Residues in contact with TYR 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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68A LEU* 4.3 20.9 - - + -
74A LEU 5.5 0.9 - - - -
79A TYR* 3.3 63.0 - + + +
80A LYS* 2.9 24.1 + - - +
97A ALA* 3.1 20.6 + - - +
100A MET* 1.3 101.2 - - + +
102A GLY* 1.3 62.0 + - - +
103A ILE* 4.2 8.1 - - + -
253B ARG* 2.8 20.9 + - - -
259B ALA* 2.4 37.8 + - + +
260B THR* 5.5 0.7 - - + -
293B MET* 5.3 3.6 - - - -
354B GLU 4.4 2.5 - - - -
357B GLY* 3.7 24.0 - - - -
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Residues in contact with GLY 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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79A TYR 4.3 0.7 - - - -
80A LYS* 3.6 24.6 - - - +
98A ILE 3.1 7.5 + - - -
99A ILE 3.1 11.5 + - - -
100A MET 3.3 1.2 + - - -
101A TYR* 1.3 79.2 - - - +
103A ILE* 1.3 60.1 + - - +
104A PRO* 3.0 17.0 - - - +
127A HIS* 4.1 8.0 - - - -
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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