Contacts of the strand formed by residues 116 - 125 (chain A) in PDB entry 1SY2
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 116 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A TRP* 3.5 5.6 - - - -
111A TYR* 3.7 8.2 - - - -
112A ALA* 3.4 0.7 - - - -
113A ASP* 2.8 56.7 + - - +
115A SER* 1.3 75.7 - - - +
117A ALA* 1.3 64.8 + - - +
137A LEU 3.3 11.7 - - - -
138A ASN* 4.0 9.6 - - - -
146A GLY 6.2 0.7 - - - -
148A LYS* 5.0 1.0 - - - +
149A VAL* 4.0 20.2 + - - +
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Residues in contact with ALA 117 (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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17A TYR* 4.0 26.7 - - + -
23A TRP* 4.2 3.4 - - + -
111A TYR* 3.2 16.4 - - - +
112A ALA* 4.1 3.1 - - + +
116A SER* 1.3 78.7 - - - +
118A LEU* 1.3 60.0 + - - +
119A ILE* 4.2 2.9 - - + -
136A VAL* 3.4 4.7 - - - -
137A LEU* 2.8 48.5 + - + +
149A VAL* 3.6 9.0 - - - +
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Residues in contact with LEU 118 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110A MET* 2.8 56.9 + - + +
111A TYR* 2.9 18.6 + - + +
117A ALA* 1.3 73.2 - - - +
119A ILE* 1.3 71.2 + - - +
134A TYR* 4.6 4.7 - - + -
135A ALA 3.5 20.9 - - - +
136A VAL* 4.1 5.8 - - + -
149A VAL* 4.1 10.5 - - + +
152A ALA* 3.9 23.8 - - + +
153A VAL* 3.9 29.6 - - + +
156A ALA* 4.6 1.1 - - + -
158A LEU* 5.3 1.3 - - + -
163A PHE* 4.4 11.9 - - + -
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Residues in contact with ILE 119 (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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17A TYR* 3.8 21.8 - - - +
107A PHE* 3.9 29.4 - - + -
108A THR 3.2 12.1 - - - +
109A VAL* 4.2 13.2 - - + -
110A MET* 4.0 5.2 - - - -
117A ALA* 4.6 0.9 - - + -
118A LEU* 1.3 81.7 - - - +
120A HIS* 1.3 74.4 + - - +
121A THR* 4.1 14.4 - - + +
134A TYR* 3.2 7.8 - - - +
135A ALA* 2.9 57.3 + - + +
137A LEU* 3.9 15.9 - - + -
185A HEM 4.2 6.3 - - + -
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Residues in contact with HIS 120 (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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2A CYS* 5.5 0.2 - - + -
4A LYS* 3.9 19.0 - - + +
6A ALA* 3.6 27.7 - - + +
106A THR* 4.5 5.5 + - - -
107A PHE* 3.5 2.1 - - - -
108A THR* 2.9 38.3 + - - +
110A MET* 3.8 9.1 - - - -
119A ILE* 1.3 77.4 - - - +
121A THR* 1.3 82.2 + - - +
122A CYS* 4.0 11.4 + - + -
132A ASP* 2.8 37.6 + - + +
133A LEU 3.5 5.2 - - - -
134A TYR* 3.7 28.3 - + + -
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Residues in contact with THR 121 (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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105A TYR* 3.6 20.4 - - - +
106A THR 2.8 19.0 + - - -
107A PHE* 4.5 2.5 - - - -
119A ILE* 4.2 14.4 - - + -
120A HIS* 1.3 82.6 - - - +
122A CYS* 1.3 61.0 + - - +
123A LEU* 4.2 3.4 + - + +
131A GLY 3.9 1.2 - - - +
132A ASP 3.8 0.3 - - - -
133A LEU* 2.8 66.1 + - + +
185A HEM 3.9 22.1 - - + +
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Residues in contact with CYS 122 (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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2A CYS* 2.0 53.8 - - + -
105A TYR* 3.2 2.9 - - - -
106A THR* 3.0 41.4 + - + +
120A HIS* 4.1 7.6 - - + -
121A THR* 1.3 76.7 + - - +
123A LEU* 1.3 59.8 + - - +
124A HIS* 3.3 31.7 - - - +
130A ALA* 3.9 2.0 - - - -
131A GLY 4.2 0.9 - - - -
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Residues in contact with LEU 123 (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 PHE* 3.6 31.4 - - + -
104A TYR 4.0 2.7 - - - +
105A TYR* 4.0 7.9 - - + -
121A THR* 4.2 3.8 + - + +
122A CYS* 1.3 71.1 - - - +
124A HIS* 1.3 72.0 + - - +
125A LYS* 4.2 7.7 + - + -
128A LYS* 4.2 22.2 + - - +
129A ALA 4.6 1.6 - - - +
130A ALA* 3.1 26.0 - - - +
131A GLY 4.5 6.2 + - - +
185A HEM 3.5 55.9 - - + +
200A NH4 4.1 12.6 - - - +
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Residues in contact with HIS 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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2A CYS* 5.2 1.3 - - + -
86A PHE* 3.8 3.6 - - - -
102A GLY* 3.1 8.0 - - - +
103A ASN* 3.4 1.4 - - - -
104A TYR* 2.8 89.9 + + + +
106A THR* 4.9 4.0 - - + +
122A CYS* 3.3 37.0 - - - +
123A LEU* 1.3 72.8 - - - +
125A LYS* 1.3 60.7 + - - +
126A GLY 5.8 1.1 - - - +
128A LYS 5.5 2.2 - - - -
130A ALA* 4.1 12.9 - - + +
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Residues in contact with LYS 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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68A PHE* 6.0 0.4 - - - -
86A PHE* 4.2 8.7 - - + -
88A LYS* 4.4 10.3 - - - +
103A ASN* 3.7 15.7 - - - +
123A LEU* 4.1 12.8 + - + +
124A HIS* 1.3 75.7 - - - +
126A GLY* 1.3 66.7 + - - +
127A ASN 3.3 0.2 + - - -
128A LYS* 3.0 34.9 + - + +
185A HEM 2.6 75.3 + - + +
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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