Contacts of the strand formed by residues 148 - 152 (chain A) in PDB entry 3SPD
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 LEU 148 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A LEU* 3.4 4.9 - - - -
74A LEU* 2.9 58.2 + - + +
100A LEU* 4.3 26.7 - - + +
101A VAL* 6.1 0.4 - - + -
104A VAL* 4.6 5.4 - - + -
135A VAL* 3.5 23.8 - - + -
136A GLY* 3.5 32.3 - - - +
137A PHE* 3.7 31.1 - - + -
147A HIS* 1.3 71.9 - - - +
149A HIS* 1.3 63.0 + - - +
150A ILE* 3.6 2.1 + - + +
177A ILE* 3.9 13.5 - - + -
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Residues in contact with HIS 149 (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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63A ASP* 4.7 2.2 - - - -
71A HIS* 2.9 31.8 + + - +
72A LEU 3.6 3.8 - - - -
73A LEU* 3.5 14.1 - - + +
134A LYS 3.7 0.6 - - - +
135A VAL* 3.2 7.8 - - - +
136A GLY 2.9 41.7 + - - +
138A HIS* 3.8 34.4 + + - -
147A HIS* 3.8 25.9 + + - -
148A LEU* 1.3 71.3 - - - +
150A ILE* 1.3 61.2 + - - +
151A MET* 4.1 6.1 - - - -
169A PHE* 3.5 23.0 - + - -
174A PHE* 3.8 14.4 - + + -
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Residues in contact with ILE 150 (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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60A LEU* 3.8 17.5 - - + -
70A MET* 3.9 17.9 - - + +
71A HIS* 3.7 0.3 - - - -
72A LEU* 2.8 44.0 + - + +
74A LEU* 3.8 27.1 - - + +
104A VAL* 3.7 24.2 - - + -
108A LEU* 5.9 0.2 - - + -
112A ILE* 4.2 23.1 - - + -
133A ILE* 4.2 13.9 - - + -
134A LYS 3.5 2.9 - - - -
135A VAL* 4.1 19.7 - - + -
148A LEU* 4.1 3.4 - - + +
149A HIS* 1.3 78.1 - - - +
151A MET* 1.3 62.0 + - - +
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Residues in contact with MET 151 (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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67A LYS* 4.0 6.3 - - + -
68A SER* 4.0 7.4 - - - +
70A MET* 3.2 21.8 - - - +
71A HIS* 3.9 24.9 - - + +
133A ILE* 3.3 2.8 - - - -
134A LYS* 2.8 54.8 + - + +
149A HIS* 4.3 11.7 - - - -
150A ILE* 1.3 77.0 - - - +
152A THR* 1.3 67.2 + - - +
155A HIS* 3.6 20.0 - - + -
169A PHE* 3.3 44.6 - - + -
174A PHE* 4.3 3.1 - - - -
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Residues in contact with THR 152 (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 SER* 2.7 22.9 + - - -
69A LYS 3.6 1.0 + - - -
70A MET* 3.1 35.0 + - + -
116A ALA* 4.5 6.3 - - + -
120A LEU* 3.8 28.1 - - + +
129A LEU* 5.2 1.3 - - + -
132A TYR* 3.1 18.4 - - + +
133A ILE* 4.1 14.1 - - + -
134A LYS* 4.3 1.7 - - - -
151A MET* 1.3 82.3 - - - +
153A LEU* 1.3 60.1 + - - +
154A ASP* 2.6 23.4 + - - -
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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