Contacts of the strand formed by residues 153 - 158 (chain H) in PDB entry 5FLX
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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144H ILE* 3.9 4.3 - - - +
145H ARG* 2.8 56.9 + - + +
147H LYS* 5.6 11.9 - - + +
151H SER* 6.4 0.4 - - - -
152H ARG* 1.3 82.2 - - - +
154H ILE* 1.3 76.5 + - - +
184H ASP* 3.6 31.2 - - + +
185H VAL* 5.9 2.0 - - - -
186H ASN* 6.3 3.8 - - + -
49W GLU* 6.0 0.7 - - - +
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Residues in contact with ILE 154 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130H LEU* 4.9 16.2 - - + -
142H LYS* 6.2 4.3 - - + -
143H ARG 4.2 2.0 - - - -
144H ILE* 3.6 31.0 - - + -
145H ARG* 5.1 1.3 - - - -
152H ARG* 5.7 5.2 - - + +
153H LEU* 1.3 88.4 - - - +
155H LYS* 1.3 71.3 + - - +
156H VAL* 5.7 4.0 - - + -
177H TYR* 5.1 8.1 - - - +
183H LYS* 5.1 13.2 - - + -
184H ASP 3.2 15.2 + - - +
185H VAL* 3.6 24.6 - - + -
186H ASN* 2.9 30.2 + - - +
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Residues in contact with LYS 155 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142H LYS* 3.6 3.1 - - - +
143H ARG* 2.7 67.8 + - - +
145H ARG* 3.2 39.2 - - + +
154H ILE* 1.3 79.3 - - - +
156H VAL* 1.3 67.1 + - - +
157H HIS* 4.0 7.9 - - - -
186H ASN* 3.5 15.3 - - + +
188H GLU* 3.4 29.1 + - + +
51W GLU* 3.0 30.3 + - - +
9b HIS* 4.7 15.4 + - - -
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Residues in contact with VAL 156 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139H ILE* 4.8 8.5 - - + -
141H GLY 3.3 12.1 - - - +
142H LYS* 3.6 26.2 - - + -
143H ARG 4.7 0.2 - - - +
154H ILE* 5.7 4.7 - - + -
155H LYS* 1.3 79.1 - - - +
157H HIS* 1.3 76.1 + - - +
158H LEU* 4.4 16.8 - - + -
186H ASN 3.6 1.6 + - - +
187H PHE* 3.5 35.7 - - + -
188H GLU* 3.4 25.8 + - - +
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Residues in contact with HIS 157 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140H VAL* 2.8 40.0 + - + -
141H GLY* 2.5 37.6 + - - +
143H ARG* 3.1 37.7 + - + +
155H LYS* 4.0 12.0 - - + -
156H VAL* 1.3 77.4 - - - +
158H LEU* 1.3 61.4 + - - +
188H GLU* 3.3 30.4 + - - -
190H PRO* 3.4 26.9 - - + +
9b HIS* 6.0 1.8 - - - -
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Residues in contact with LEU 158 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134H VAL* 3.9 31.0 - - + -
137H SER* 5.2 2.2 - - - +
138H GLU 3.4 18.6 - - - +
139H ILE* 3.9 16.2 - - + -
140H VAL* 3.4 11.5 - - - +
156H VAL* 4.4 14.1 - - + -
157H HIS* 1.3 82.2 - - - +
159H ASP* 1.3 66.3 + - - +
160H LYS 3.7 0.7 + - - -
187H PHE* 4.6 16.8 - - + -
188H GLU 3.3 10.9 + - - +
189H PHE* 3.5 44.9 - - + -
190H PRO* 4.0 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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