Contacts of the strand formed by residues 153 - 157 (chain A) in PDB entry 3FIE
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 153 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A ASN 2.9 7.2 + - - +
43A VAL* 3.3 25.1 - - + -
44A TRP 2.9 26.5 + - - +
111A ILE* 4.1 17.0 - - + -
151A LEU* 3.6 6.8 - - - +
152A ASN* 1.3 81.4 - - + +
154A LEU* 1.3 65.5 + - - +
155A VAL* 4.7 5.2 - - + -
191A ASN* 3.0 36.1 - - + +
193A VAL* 3.4 28.7 - - + -
229A LEU* 3.4 33.2 - - + -
232A ALA* 4.0 7.4 - - + -
236A LEU* 5.1 2.7 - - + -
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A MET* 3.9 26.7 - - - -
25A PRO* 3.5 37.5 - - + -
44A TRP* 3.5 15.9 - - + +
46A ILE* 4.0 21.8 - - + -
137A VAL* 5.2 3.6 - - + -
151A LEU* 4.2 10.9 - - + +
153A LEU* 1.3 74.8 - - - +
155A VAL* 1.3 70.5 + - - +
156A LEU* 4.0 14.9 + - + -
190A ILE* 4.7 2.2 - - + -
191A ASN 3.0 7.4 + - - +
192A ILE* 3.5 19.7 - - + +
193A VAL 2.9 24.1 + - - -
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Residues in contact with VAL 155 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A ILE* 4.5 13.7 - - + -
43A VAL* 4.7 1.6 - - + -
44A TRP 2.9 17.1 + - - +
45A ILE* 3.5 17.5 - - + +
46A ILE 3.0 26.9 + - - +
87A TYR* 3.6 19.5 - - - +
91A THR* 4.8 5.2 - - + -
95A PHE* 4.6 16.2 - - + -
153A LEU* 4.7 9.4 - - + -
154A LEU* 1.3 77.0 - - - +
156A LEU* 1.3 67.0 + - - +
193A VAL* 3.2 22.2 - - + +
195A PHE* 4.1 14.6 - - + -
225A LEU* 5.8 2.0 - - + -
229A LEU* 5.9 0.4 - - + -
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Residues in contact with LEU 156 (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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24A ILE* 3.4 35.2 - - + -
46A ILE* 3.6 26.2 - - + +
48A GLU 4.2 4.7 - - - +
49A ARG 5.5 0.4 - - - +
50A ASN* 3.6 39.9 - - + +
52A ILE* 4.1 12.3 - - + -
87A TYR* 3.0 13.8 + - - -
154A LEU* 4.4 14.6 - - + -
155A VAL* 1.3 76.0 - - - +
157A GLY* 1.3 68.1 + - - +
192A ILE* 3.8 15.7 - - + -
193A VAL 2.9 8.0 + - - +
194A THR* 3.5 0.9 - - - -
195A PHE 3.0 20.1 + - - -
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Residues in contact with GLY 157 (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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46A ILE 3.8 4.0 + - - -
48A GLU 2.7 21.7 + - - -
49A ARG* 4.2 0.7 - - - -
50A ASN* 3.2 16.6 + - - +
77A TYR* 5.7 0.2 - - - -
78A LEU* 3.7 11.4 - - - -
87A TYR* 3.4 20.7 + - - -
156A LEU* 1.3 76.8 - - - +
158A ALA* 1.3 69.2 + - - +
194A THR* 3.4 3.5 - - - +
195A PHE 3.8 1.3 - - - -
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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