Contacts of the strand formed by residues 105 - 110 (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 ARG 105 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A THR* 3.5 35.8 + - - +
6A MET 4.9 0.2 + - - -
7A ALA* 4.7 3.0 - - - +
8A SER* 3.5 12.3 - - - +
11A ASP* 3.0 41.0 + - - -
40A ASN* 4.7 9.0 - - - +
82A THR 3.7 1.2 + - - +
83A THR* 3.0 40.6 + - + +
84A LEU* 2.9 24.2 + - - -
98A ILE* 5.6 0.2 - - - -
103A ILE* 3.4 9.5 - - - +
104A PRO* 1.3 92.7 - - + +
106A CYS* 1.3 61.8 + - - +
107A VAL* 4.1 4.6 - - - +
127A HIS* 5.9 0.2 - - - -
128A GLU* 2.9 33.5 + - + +
130A VAL* 4.0 21.1 - - + +
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Residues in contact with CYS 106 (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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84A LEU* 3.3 10.3 - - + -
86A THR* 4.1 12.8 - - - -
90A PRO* 4.5 3.6 - - - -
98A ILE* 3.7 34.8 - - + -
105A ARG* 1.3 75.6 - - - +
107A VAL* 1.3 62.8 + - - +
108A VAL* 3.9 21.0 + - - -
122A LEU* 4.3 18.2 - - + -
127A HIS* 6.1 0.9 - - + -
128A GLU 3.0 10.4 + - - +
129A VAL* 3.4 7.0 - - + +
130A VAL* 3.0 24.1 + - - +
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Residues in contact with VAL 107 (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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11A ASP* 3.7 18.2 - - + +
15A MET* 3.6 19.6 - - + +
83A THR* 3.6 21.8 - - + -
84A LEU 2.9 6.5 + - - +
85A TYR* 3.4 25.0 - - + -
86A THR* 3.0 27.3 + - - +
105A ARG* 4.0 14.1 - - - +
106A CYS* 1.3 73.9 - - - +
108A VAL* 1.3 61.0 + - - +
130A VAL* 3.4 16.8 - - + +
132A VAL* 3.7 18.6 - - + -
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Residues in contact with VAL 108 (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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15A MET* 3.8 3.1 - - - -
86A THR* 3.4 8.5 - - + -
88A LEU 3.7 2.2 - - - -
89A SER* 3.2 35.9 - - - +
90A PRO* 4.0 11.2 - - + -
106A CYS* 3.9 20.9 - - - -
107A VAL* 1.3 76.7 - - - +
109A GLY* 1.3 63.5 + - - +
110A GLU* 3.3 16.6 - - - +
119A GLU* 5.5 0.2 - - + -
129A VAL* 4.4 14.1 - - + -
130A VAL 2.6 16.1 + - - +
131A VAL* 3.5 11.3 - - + -
132A VAL* 2.8 30.8 + - - +
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Residues in contact with GLY 109 (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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15A MET* 3.6 21.0 - - - +
86A THR 2.8 14.3 + - - -
87A THR* 3.5 10.5 + - - -
108A VAL* 1.3 73.3 - - - +
110A GLU* 1.3 56.9 + - - +
132A VAL* 4.5 1.1 - - - -
133A ASP 2.7 12.5 + - - -
134A ASP* 2.7 39.0 + - - -
137A CYS* 4.5 1.6 - - - -
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Residues in contact with GLU 110 (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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87A THR 3.3 13.4 + - - +
88A LEU* 3.3 23.9 - - - +
89A SER 2.9 24.3 + - - -
108A VAL* 3.4 5.5 - - - -
109A GLY* 1.3 79.6 - - - +
111A ASN* 1.3 60.6 + - - +
112A VAL* 2.8 34.2 + - - +
113A ASN* 2.7 33.7 + - - +
131A VAL* 4.4 6.7 - - - -
133A ASP* 4.4 13.7 - - - +
134A ASP 4.4 6.5 - - - +
137A CYS* 4.3 1.3 - - + -
138A LYS* 3.5 27.7 - - - +
141A MET* 3.7 7.8 - - - +
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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