Contacts of the strand formed by residues 133 - 138 (chain B) 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 ILE 133 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B MET* 4.1 14.4 - - + -
104B VAL* 6.3 0.7 - - + -
112B ILE* 4.2 15.3 - - + -
113B PHE* 4.3 15.0 - - + -
116B ALA* 4.5 5.8 - - + -
129B LEU* 3.2 28.3 - - + +
130B ALA* 3.7 13.7 + - - +
131B ASN 3.6 1.6 - - - -
132B TYR* 1.3 83.2 - - - +
134B LYS* 1.3 70.3 + - - +
135B VAL* 4.2 9.1 - - + +
150B ILE* 4.1 19.3 - - + -
151B MET 3.3 8.3 - - - +
152B THR* 4.1 13.7 - - + -
153B LEU* 4.0 4.3 - - - +
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Residues in contact with LYS 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B ILE* 1.3 74.1 - - - +
135B VAL* 1.3 65.8 + - - +
136B GLY 4.4 0.2 - - - -
149B HIS 3.7 1.0 - - - +
150B ILE* 3.5 0.9 - - - -
151B MET* 2.8 59.8 + - + +
152B THR 4.2 3.1 - - - -
153B LEU* 3.7 26.3 + - + +
155B HIS* 2.8 34.8 + - - -
169B PHE* 2.9 22.9 + - - +
170B THR* 3.9 5.9 - - - +
174B PHE* 3.9 22.2 - - + -
176B LYS* 4.5 20.9 - - - +
201B TRP* 6.0 1.4 - - - +
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Residues in contact with VAL 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B VAL* 6.2 0.7 - - + -
104B VAL* 4.4 20.2 - - + -
133B ILE* 4.2 14.6 - - + +
134B LYS* 1.3 83.6 - - - +
136B GLY* 1.3 60.2 + - - +
148B LEU* 3.6 30.5 - - + -
149B HIS 3.2 5.6 - - - +
150B ILE* 4.2 17.7 - - + -
174B PHE* 3.8 3.1 - - - -
176B LYS* 3.4 9.3 - - - +
177B ILE* 2.9 39.5 + - + +
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Residues in contact with GLY 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135B VAL* 1.3 77.2 - - - +
137B PHE* 1.3 59.3 + - - -
148B LEU* 3.5 12.6 - - - -
149B HIS* 2.8 39.7 + - - +
174B PHE* 3.3 15.1 - - - -
175B VAL 3.2 12.8 - - - -
177B ILE 3.9 2.7 - - - -
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Residues in contact with PHE 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.6 30.5 - - + -
89B ILE* 4.5 10.8 - - + -
90B MET* 3.9 25.6 - - + -
97B VAL* 5.4 0.2 - - + -
100B LEU* 4.1 20.4 - - + -
136B GLY* 1.3 73.8 - - - -
138B HIS* 1.3 62.4 + - - +
146B LEU* 3.7 29.4 - - + -
147B HIS 3.4 14.4 - - - -
148B LEU* 3.7 32.1 - - + -
149B HIS* 4.4 2.5 - - - -
173B PHE 3.6 0.5 - - - +
174B PHE* 3.6 3.9 - - - -
175B VAL* 2.7 46.0 + - + +
177B ILE* 3.6 22.2 - - + -
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Residues in contact with HIS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B PRO* 3.4 22.3 - - - +
87B LEU* 5.8 0.2 - - - +
137B PHE* 1.3 77.1 - - - +
139B ALA* 1.3 62.9 - - - +
140B GLY 3.4 0.3 + - - -
141B PRO* 3.6 21.6 - - + +
147B HIS* 5.2 1.6 + - - -
149B HIS* 3.8 17.8 + + - +
168B SER* 3.2 45.3 + - - -
169B PHE* 3.4 35.4 - + - -
173B PHE* 3.5 17.5 - + + -
174B PHE* 4.2 6.7 - + - -
175B VAL* 4.7 0.4 - - - -
1F G 4.0 10.8 - - - -
2F T 3.6 18.4 + - - -
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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