Contacts of the strand formed by residues 190 - 195 (chain E) in PDB entry 5FLM
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 VAL 190 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150E VAL* 4.2 2.8 - - - +
151E MET* 3.2 43.6 + - - +
156E VAL* 3.8 37.2 - - + +
159E LEU* 4.5 4.0 - - + -
160E LEU* 6.2 0.2 - - + -
167E GLU* 6.3 1.6 - - + -
170E LEU* 4.3 16.6 - - + -
188E GLY 4.4 2.7 - - - +
189E GLN* 1.3 78.1 - - - +
191E VAL* 1.3 76.5 + - - +
206E TYR* 4.2 16.2 - - + -
207E ARG 3.6 9.0 - - - +
208E LEU* 3.7 20.2 - - + -
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Residues in contact with VAL 191 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148E HIS* 4.9 10.3 - - + -
149E VAL 3.8 7.0 - - - +
150E VAL* 4.4 8.7 - - + -
151E MET* 4.6 0.4 - - - -
173E ILE* 4.1 13.9 - - + -
185E ILE* 3.5 34.3 - - + -
190E VAL* 1.3 80.1 - - - +
192E LYS* 1.3 59.5 + - - +
193E ILE* 3.6 14.5 + - + -
205E THR 3.7 0.9 - - - +
206E TYR* 3.3 6.8 - - - -
207E ARG* 2.9 58.4 + - + +
209E VAL* 4.2 12.1 - - + -
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Residues in contact with LYS 192 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1029A LEU* 5.5 4.9 - - - +
1032A GLN* 5.7 4.8 - - - +
147E GLU 3.7 2.4 - - - +
148E HIS* 4.6 0.2 - - - -
149E VAL* 2.9 56.4 + - + +
151E MET* 3.7 21.1 - - + +
155E GLU* 6.0 1.3 - - - +
191E VAL* 1.3 72.2 - - - +
193E ILE* 1.3 60.9 + - - +
194E ILE* 3.9 20.3 + - + +
204E ILE* 3.9 35.9 - - + +
205E THR 3.5 3.4 - - - -
206E TYR* 3.8 23.8 + - + -
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Residues in contact with ILE 193 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1372A GLU* 4.2 17.9 - - + +
146E PRO* 3.5 29.2 - - + -
147E GLU 3.4 3.4 - - - +
148E HIS* 3.4 29.6 - - + +
173E ILE* 5.6 1.8 - - + -
191E VAL* 3.6 22.4 - - + +
192E LYS* 1.3 72.0 - - - +
194E ILE* 1.3 66.7 + - - +
195E ARG* 4.3 15.0 - - + +
203E TYR 3.7 0.5 - - - +
204E ILE* 3.3 7.3 - - - +
205E THR* 2.9 40.5 + - - +
207E ARG* 3.6 31.4 - - + -
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Residues in contact with ILE 194 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E PRO* 3.6 0.7 - - - +
147E GLU* 2.9 51.8 + - + +
149E VAL* 4.8 16.2 - - + -
192E LYS* 4.4 23.6 - - + +
193E ILE* 1.3 75.8 - - - +
195E ARG* 1.3 64.1 + - - +
196E PRO* 4.4 2.6 - - + +
202E ARG* 3.8 34.1 - - + +
203E TYR 3.7 2.9 - - - +
204E ILE* 4.3 14.8 - - + -
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Residues in contact with ARG 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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893A GLU* 2.9 28.9 + - - -
1372A GLU* 4.2 17.1 + - - -
1375A ARG* 4.3 17.4 - - - +
1376A LYS* 5.2 13.9 - - - +
1403A ASP* 4.2 17.6 + - - -
146E PRO* 3.6 20.4 - - + -
193E ILE* 3.9 6.1 - - + +
194E ILE* 1.3 75.6 - - - +
196E PRO* 1.3 73.9 - - + +
197E SER* 3.7 1.0 + - - -
202E ARG* 4.6 3.4 - - - -
203E TYR* 2.9 56.3 + - + +
205E THR* 2.3 33.5 + - - +
207E ARG* 5.5 2.4 - - - +
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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